University of Groningen

Structure and dynamics of peptidesvan der Spoel, David

IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.

Document VersionPublisher's PDF, also known as Version of record

Publication date:1996

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):van der Spoel, D. (1996). Structure and dynamics of peptides: theoretical aspects of protein folding. s.n.

CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).

Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.

Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.

Download date: 02-01-2020

Bibliography

[1] Schulz, G. E., Schirmer, R. H. Principles of Protein structure. New York: Springer Verlag.

1978.

[2] Stryer, L. Biochemistry. 3 Ed. New York: Freeman. 1988: 211.

[3] Babu, Y. S., Bugg, C. E., Cook, W. J. Structure of calmodulin re�ned at 2.2�A. J. Mol.

Biol. 204:191{204, 1988.

[4] Sicheri, F., Yang, D. S. C. Ice-binding structure and mechanism of an antifreeze protein

from winter ounder. Nature 375:427{431, 1995.

[5] van Nuland, N., Hangyi, I. W., van Schaik, R. C., Berendsen, H. J. C., van Gunsteren,

W. F., Scheek, R. M., Robillard, G. T. The high-resolution structure of the histidine-

containing phosphocarrier protein HPr from Escherichia coli determined by restrained

molecular dynamics from NMR nuclear overhauser e�ect data. J. Mol. Biol. 237:544{559,

1994.

[6] Burley, S. K., Petsko, G. A. Electrostatic interactions in aromatic oligopeptides contribute

to protein stability. Trends Biotech. 7:354{359, 1989.

[7] Atkins, P. W. Physical Chemistry. Fourth edition Ed. Oxford, UK: Oxford University

Press. 1990.

[8] Besler, B. H., Merz Jr., K. M., Kollman, P. A. Atomic charges derived from semiempirical

methods. J. Comp. Chem. 11:431{439, 1990.

[9] Weiner, S. J., Kollman, P. A., Nguyen, D. T., Case, D. A. An all atom force �eld for

simulation of proteins and nucleic acids. J. Comp. Chem. 7:230{252, 1986.

[10] Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., Karplus,

M. CHARMM: a program for macromolecular energy, minimization, and dynamics calcu-

lation. J. Comp. Chem. 4:187{217, 1983.

[11] van Gunsteren, W. F., Berendsen, H. J. C. Gromos-87 manual. Biomos BV Nijenborgh 4,

9747 AG Groningen, The Netherlands 1987.

[12] Jorgensen, W. L., Tirado-Rives, J. The OPLS potential functions for proteins. energy

minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657{

1666, 1988.

[13] van der Spoel, D., van Buuren, A. R., Apol, E., Meulenho�, P. J., Tieleman,

D. P., Sijbers, A. L. T. M., van Drunen, R., Berendsen, H. J. C. Gromacs User

Manual version 1.3. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet:

http://rugmd0.chem.rug.nl/�gmx 1996.

[14] Privalov, P. L. Physical basis of the stability of folded conformations of proteins. In:

Protein Folding. Creighton, T. E. ed. . Freeman 1992 83{126.

[15] An�nsen, C. B. Principles that govern the folding of protein chains. Science 181:223{230,

1973.

130 BIBLIOGRAPHY

[16] Levinthal, C. Are there pathways for protein folding ? J. Chim. Phys. 65:44{45, 1968.

[17] Drenth, J. Principles of Protein X-ray Crystallography. New York: Springer. 1994.

[18] Miller, R. T., Jones, D. T., Thronton, J. M. Protein fold recognition by sequence threading:

Tools and assessment techniques. FASEB J. 10:171{177, 1996.

[19] Lathrop, R. H., Smith, T. F. Global optimum protein threading with gapped alignment

and empirical pair score functions. J. Mol. Biol. 255:641{666, 1996.

[20] Karplus, M., Shakhnovich, E. Protein folding: Theoretical studies of thermodynamics and

dynamics. In: Protein Folding. Creighton, T. E. ed. . Freeman 1992 127{196.

[21] Schmid, F. X. Kinetics of unfolding and refolding of single-domain proteins. In: Protein

Folding. Creighton, T. E. ed. . Freeman 1992 197{241.

[22] Ohgushi, M., Wada, A. 'Molten-globule state': a compact form of globular proteins with

mobile side-chains. FEBS Lett. 164:21{24, 1983.

[23] Kuwajima, K. The molten globule state as a clue for understanding the folding and

cooperativity of globular-protein structure. PROTEINS: Struct. Funct. Gen. 6:87{103,

1989.

[24] Ptitsyn, O. B., Pain, R. H., Semisotnov, G. V., Zerovnik, E., Razgulyaev, O. I. Evidence for

a molten globule state as a general intermediate in protein folding. FEBS Lett. 262:20{24,

1990.

[25] Sosnick, T. R., Mayne, L., Hiller, R., Englander, S. W. The barriers in protein folding.

Nature Struct. Biol. 1:149{156, 1994.

[26] Creighton, T. E. The energetic ups and downs of protein folding. Nature Struct. Biol.

1:135{138, 1994.

[27] Baldwin, R. L. The nature of protein folding pathways: The classical versus the new view.

J. Biomol. NMR 5:103{109, 1995.

[28] Privalov, P. L. Intermediate states in protein folding. J. Mol. Biol. 258:707{725, 1996.

[29] Baldwin, R. L. Why is protein folding so fast ? Proc. Natl. Acad. Sci. USA 93:2627{2628,

1996.

[30] Williams, S., Casgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodru�,

W. H., Dyer, R. B. Fast events in protein folding: Helix melting and formation in a small

peptide. Biochemistry 35:691{697, 1996.

[31] Frydman, J., Nimmesgern, E., Ohtsuka, K., Hartl, F. U. Folding of nascent polypetide

chains in a high molecular mass assembly with molecular chaperones. Nature 370:111{117,

1994.

[32] Fedorov, A. N., Baldwin, T. O. Contribution of cotranslational folding to the rate of

formation of native protein structure. Proc. Natl. Acad. Sci. USA 92:1227{1231, 1995.

[33] Jaenicke, R. What does protein refolding in vitro tell us about protein folding in the cell?

Phil. Trans. R. Soc. Lond 339:287{295, 1993.

[34] Dill, K. A., Fiebig, K. M., Chan, H. S. Cooperativity in protein-folding kinetics. Proc.

Natl. Acad. Sci. USA 90:1942{1946, 1993.

BIBLIOGRAPHY 131

[35] Dill, K. A. Folding proteins: �nding a needle in a haystack. Curr. Opin. Struct. Biol.

3:99{103, 1993.

[36] Tirado-Rives, J., Jorgensen, W. L. Molecular dynamics simulations of the unfolding of an

�-helical analogue of ribonuclease A S-peptide in water. Biochemistry 30:3864{3871, 1991.

[37] Mark, A. E., van Gunsteren, W. F. Simulation of the thermal denaturation of hen egg

white lysozym: Trapping the molten globule state. Biochemistry 31:7745{7748, 1992.

[38] Daggett, V., Levitt, M. A model of the molten globule state from molecular dynamics

simulations. Proc. Natl. Acad. Sci. USA 89:5142{5146, 1992.

[39] Daggett, V., Levitt, M. Molceular dynamics simulations of helix denaturation. J. Mol.

Biol. 223:1121{1138, 1992.

[40] van Buuren, A. R., Berendsen, H. J. C. Molecular dynamics simulation of the stability of

a 22 residue alpha-helix in water and 30 % tri uoroethanol. Biopolymers 33:1159{1166,

1993.

[41] Brooks III, C. L. Molecular simulations of peptide and protein unfolding: in quest of a

molten globule. Curr. Opin. Struct. Biol. 3:92{98, 1993.

[42] Tirado-Rives, J., Jorgensen, W. L. Molecular dynamics simulations of the unfolding of

apomyoglobin in water. Biochemistry 33:4175{4184, 1993.

[43] Ca isch, A., Karplus, M. Molecular dynamics studies of protein and peptide folding and

unfolding. In: The Protein Folding Problem and Tertiary Structure Prediction. Merz Jr.,

K. M., Le Grand, S. M. eds. . Birkh�auser Boston 1994 193{230.

[44] Kazmirski, S. L., Alonso, D. O. V., Cohen, F. E., Prusiner, S. B., Daggett, V. Theoretical

studies of sequence e�ects on the conformational properties of a fragment of the prion

protein: implications for scrapie formation. Curr. Biol. 2:305{315, 1995.

[45] Kirshenbaum, K., Daggett, V. pH-dependent conformations of the amyloid �(1-28) peptide

fragment explored using molecular dynamics. Biochemistry 34:7629{7639, 1995.

[46] Kirshenbaum, K., Daggett, V. Sequence e�ects on the conformational properties of the

amyloid �(1-28) peptide: Testing a proposed mechanism for tha � ! � transition. Bio-

chemistry 34:7640{7647, 1995.

[47] van der Spoel, D., Vogel, H. J., Berendsen, H. J. C. Molecular dynamics simulations of

N-terminal peptides from a nucleotide binding protein. PROTEINS: Struct. Funct. Gen.

24:450{466, 1996.

[48] Levitt, M., Warshel, A. Computer simulation of protein folding. Nature 253:694{698, 1975.

[49] Vieth, M., Kolinski, A., Brooks III, C. L., Skolnick, J. Prediction of the folding pathways

and structure of the GCN4 leucine zipper. J. Mol. Biol. 237:361{367, 1994.

[50] Srinivasan, R., Rose, G. D. LINUS: A hierarchic procedure to predict the fold of a protein.

PROTEINS: Struct. Funct. Gen. 22:81{99, 1995.

[51] Bekker, H., Berendsen, H. J. C., Dijkstra, E. J., Achterop, S., van Drunen, R., van der

Spoel, D., Sijbers, A., Keegstra, H., Reitsma, B., Renardus, M. K. R. Gromacs: A parallel

computer for molecular dynamics simulations. In Physics Computing 92 (Singapore, 1993).

de Groot, R. A., Nadrchal, J., eds. . World Scienti�c.

132 BIBLIOGRAPHY

[52] Berendsen, H. J. C., van der Spoel, D., van Drunen, R. GROMACS: A message-passing

parallel molecular dynamics implementation. Comp. Phys. Comm. 91:43{56, 1995.

[53] Allen, M. P., Tildesley, D. J. Computer Simulations of Liquids. Oxford: Oxford Science

Publications. 1987.

[54] Kemmink, J., van Mierlo, C. P. M., Scheek, R. M., Creighton, T. E. Local structure due

to an aromatic-amide interaction observed by 1H-nuclear magnetic resonance spectroscopy

in peptides related to the N terminus of bovine pancreatic trypsin inhibitor. J. Mol. Biol.

230:312{322, 1993.

[55] Br�unger, A. T. X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR. New

Haven: Yale University Press. 1992.

[56] van Gunsteren, W. F., Berendsen, H. J. C. Computer simulation of molecular dynamics:

Methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl.

29:992{1023, 1990.

[57] van Gunsteren, W. F., Karplus, M. E�ect of constraints, solvent and crystal environment

on protein dynamics. Nature 293:677{678, 1981.

[58] Heiner, A. P., Berendsen, H. J. C., van Gunsteren, W. F. MD simulation of subtilisin

BPN' in a crystal environment. PROTEINS: Struct. Funct. Gen. 14:451{464, 1992.

[59] van Gunsteren, W. F., Mark, A. E. On the interpretation of biochemical data by molecular

dynamics simulation. Eur. J. Biochem. 204:947{961, 1991.

[60] Morikami, K., Saito, M. Molecular dynamics study on the stability of ions around human

lysozyme in the crystal condition. Comp. Phys. Comm. 225:196{201, 1994.

[61] van Nuland, N. A. J., Wiersma, J. A., van der Spoel, D., de Groot, B. L., Scheek, R. M.,

Robillard, G. T. Phosphorylation-induced torsion-angle strain in the active center of hpr,

detected by nmr and restrained molecular dynamics re�nement. Prot. Sci. 5:442{446, 1996.

[62] Heidorn, D. B., Trewhella, J. Comparison of the crystal and solution structures of calmod-

ulin and troponin C. Biochemistry 27:909{915, 1988.

[63] Ikura, M., Spera, S., Barbato, G., Kay, L. E., Krinks, M., Bax, A. Secondary structure and

side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear

multidimensional NMR spectroscopy. Biochemistry 30:9216{9228, 1991.

[64] Torda, A. E., van Gunsteren, W. F. Algorithms for clustering molecular dynamics con�g-

urations. J. Comp. Chem. 15(12):1331{1340, 1994.

[65] Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of

hydrogen-bonded and geometrical features. Biopolymers 22:2577{2637, 1983.

[66] Wright, P. E., Dyson, H. J., Lerner, R. A. Conformation of peptide fragments of proteins in

aqueous solution: Implications for initiation of protein folding. Biochemistry 27:7167{7175,

1988.

[67] Hirst, J. D., Brooks III, C. L. Molecular dynamics simulations of isolated helices of myo-

globin. Biochemistry 34:7614{7621, 1995.

[68] Hayward, S., G�o, N. Collective variable description of native protein dynamics. Annu.

Rev. Phys. Chem. 46:223{250, 1995.

BIBLIOGRAPHY 133

[69] Elofsson, A., Nilsson, L. How consistent are molecular dyanamics simulations ? J. Mol.

Biol. 233:766{780, 1993.

[70] H�unenberger, P. H., Mark, A. E., van Gunsteren, W. F. Fluctuation and cross-correlation

analysis of protein motions observed in nanosecond molecular dynamics simulations. J.

Mol. Biol. 252:492{503, 1995.

[71] Storch, E. M., Daggett, V. Molecular dynamics simulation of cytochrome b5: Implications

for protein-protein recognition. Biochemistry 34:9682{9693, 1995.

[72] Wishart, D. S., Sykes, B. D. Chemical shifts as a tool for structure determination. Methods

in Enyzmology 239:363{391, 1994.

[73] Merutka, G., Dyson, H. J., Wright, P. E. 'Random coil' 1H chemical shifts obtained as a

function of temperature and tri uoroethanol concentration for the peptide series GGXGG.

J. Biomol. NMR 5:14{24, 1995.

[74] Bundi, A., W�uthrich, K. 1H-NMR parameters of the common amino acid residues mea-

sured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers

18:285{297, 1979.

[75] Khaled, M. A., Long, M. M., Thompson, W. D., Bradley, R. J., Brown, G. B., Urry,

D. W. Conformational states of enkephalins in solution. Biochem. Biophys. Res. Comm.

76:224{231, 1977.

[76] Gauss, J. E�ects of electron correlation in the calculation of nuclear magnetic resonance

chemical shifts. J. Chem. Phys. 99:3629{3643, 1993.

[77] Pearson, J. G., Wang, J. F., Markley, J. L., Le, H. B., Old�eld, E. Protein structure

re�nement using carbon-13 nuclear magnetic resonance spectroscopic chemical shifts and

quantum chemistry. J. Am. Chem. Soc. 117:8823{8829, 1995.

[78] de Dios, A. C., Pearson, J. G., Old�eld, E. Secondary and tertiary structural e�ects on

protein NMR chemical shifts: An ab initio approach. Science 260:1491{1496, 1995.

[79] Gauss, J. Accurate calculation of NMR chemical shifts. Ber. Bunsenges. Phys. Chem.

99:1001{1008, 1995.

[80] Frisch, M. J., Trucks, G. W., Schlegel, H. B., Gill, P. M. W., Johnson, B. G., Robb, M. A.,

Cheeseman, J. R., Keith, T. A., Petersson, G. A., Montgomery, J. A., Raghavachari, K.,

Al-Laham, M. A., Zakrzewski, V. G., Ortiz, J. V., Foresman, J. B., Ciosloswki, J., Stefanof,

B. B., Nanayakkara, A., Challacombe, M., Peng, C. Y., Ayala, P. Y., Chen, W., Wong,

M. W., Andres, J. L., Replogle, E. S., Gomperts, R., Martin, R. L., Fox, D. J., Binkley,

J. S., Defrees, D. J., Baker, J., Stewart, J. P., Head-Gordon, M., Gonzalez, C., Pople, J. A.

Gaussian 94, revision A.1. Gaussian, Inc. Pittsburgh PA 1995.

[81] Spera, S., Bax, A. Empirical correlation between protein backbone conformation and C�and C�

13C nuclear magnetic resonance chemical shifts. J. Am. Chem. Soc. 113:5490{5492,

1991.

[82] �Osapay, K., Case, D. A. A new analysis of proton chemical shifts. J. Am. Chem. Soc.

113:9436{9444, 1991.

[83] Williamson, M. P., Asakura, T. Empirical comparisons of models for chemical-shift calcu-

lation in proteins. J. Magn. Reson. Ser. B 101:63{71, 1993.

134 BIBLIOGRAPHY

[84] Case, D. A. Calibration of ring-current e�ects in proteins and nucleic acids. J. Biomol.

NMR 6:341{346, 1995.

[85] Case, D. A., Dyson, H. J., Wright, P. E. Use of chemical shifts and coupling constants

in nuclear magnetic resonance structural studies on peptides and proteins. Methods in

Enyzmology 239:392{415, 1994.

[86] �Osapay, K., Theriault, Y., Wright, P. E., Case, D. A. Solution structure of carbonmonoxy

myoglobin determined from nuclear magnetic resonance distance and chemical shift con-

straints. J. Mol. Biol. 244:183{197, 1994.

[87] Kuszewski, J., Qin, J., Gronenborn, A. M., Clore, G. M. The impact of direct re�nement

against 13C� and 13C� chemical shifts on protein structure determination by NMR. J.

Magn. Reson. Ser. B 106:92{96, 1995.

[88] Kuszewski, J., Gronenborn, A. M., Clore, G. M. The impact of direct re�nement against

proton chemical shifts on protein structure determination by NMR. J. Magn. Reson. Ser.

B 107:293{297, 1995.

[89] Celda, B., Biamonti, C., Arnau, M. J., Tejero, R., Montelione, G. T. Combined use of13C chemical shifts and 1H�-13C� heteronuclear NOE data in monitoring a protein NMR

structure re�nement. J. Biomol. NMR 5:161{172, 1995.

[90] Karplus, M. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys.

30:11{15, 1959.

[91] Pardi, A., Billeter, M., W�uthrich, K. Calibration of the angular dependence of the amide

proton-C� proton coupling constants 3JHN�, in a globular protein. J. Mol. Biol. 180:741{

751, 1984.

[92] Smith, L. J., Sutcli�e, M. J., Red�eld, C., Dobson, C. M. Analysis of � and �1 torsion angles

for hen lysozyme in solution from 1H NMR spin-spin coupling constants. Biochemistry

30:986{996, 1991.

[93] Ludvigsen, S., Andersen, K. V., Poulsen, F. M. Accurate measurements of coupling con-

stants from two-dimensional nuclear magnetic resonance spectra of proteins and determi-

nation of �-angles. J. Mol. Biol. 217:731{736, 1991.

[94] Vuister, G. W., Bax, A. Quantitative J correlation: A new approach for measuring homonu-

clear three-bond J(HN -H�) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc.

115:7772{7777, 1993.

[95] DeMarco, A., Llinas, M., W�uthrich, K. Analysis of the 1H-NMR spectra of ferrichrome

peptides. i. the non-amide proteins. Biopolymers 17:617{636, 1978.

[96] Wang, A. C., Bax, A. Reparametrization of the Karplus relation for 3J(H�-N) and 3J(HN -

C') in peptides from uniformly 13C15N-enriched human ubiquitin. J. Am. Chem. Soc.

117:1810{1813, 1995.

[97] Bystrov, V. F. Spin-spin coupling and the conformational states of peptide systems. Progr.

NMR Spectr. 10:41{81, 1976.

[98] Vuister, G. W., Delaglio, F., Bax, A. An empirical correlation between 1JC�H� and protein

backbone conformation. J. Am. Chem. Soc. 114:9674{9675, 1992.

BIBLIOGRAPHY 135

[99] Brunne, R. M., van Gunsteren, W. F., Br�uschweiler, R., Ernst, R. R. Molecular dynamics

simulation of the proline conformational equilibrium and dynamics in antamanide using

the GROMOS force �eld. J. Am. Chem. Soc. 4764{4768, 1993.

[100] Schmidt, J. M., Br�uschweiler, R., Ernst, R. R., Dunbrack Jr. , R. L., Joseph, D., Karplus,

M. Molecular dynamics simulation of the proline conformational equilibrium and dynamics

in antamanide using the CHARMM force �eld. J. Am. Chem. Soc. 8747{8756, 1993.

[101] Liu, Z.-P., Gierasch, L. M. Combined use of molecular dynamics simulations and NMR to

explore peptide bond isomerization and multiple intramolecular hydrogen-bonding possi-

bilites in a cyclic pentapeptide, cyclo(gly-pro-D-phe-gly-val). Biopolymers 32:1727{1739,

1992.

[102] Kim, Y., Prestegard, J. H. Re�nement of NMR structures for acyl carrier protein with

scalar coupling data. PROTEINS: Struct. Funct. Gen. 8:377{385, 1990.

[103] Torda, A. E., Brunne, R. M., Huber, T., Kessler, H., van Gunsteren, W. F. Structure

re�nement using time-averaged J-coupling constant restraints. J. Biomol. NMR 3:55{66,

1993.

[104] Abragam, A. Principles of Nuclear Magnetism. Oxford, UK: Oxford University Press. 1961.

[105] Macura, S., Ernst, R. R. Elucidation of cross relaxation in liquids by two-dimensional

NMR spectroscopy. Mol. Phys. 41:95{117, 1980.

[106] Tropp, J. Dipolar relaxation and nuclear overhauser e�ects in nonrigid molecules: The

e�ect of uctuating internuclear distances. J. Chem. Phys. 72:6035{6043, 1980.

[107] Lipari, G., Szabo, A. Model-free approach to the interpretation of nuclear magnetic res-

onance relaxation in macromolecules. 1. theory and range of validity. J. Am. Chem. Soc.

104:4546{4559, 1982.

[108] Tissen, J. T. W. M., Drenth, J., Berendsen, H. J. C., Fraaije, J. G. E. M. Microhydrody-

namics simulation of protein crystallization. I. static calculations. Biophys. J. 67:1801{1805,

1994.

[109] Smith, P. E., van Schaik, R. C., Szyperski, T., W�uthrich, K., van Gunsteren, W. F. Internal

mobility of the basic pancreatic trypsin inhibitor in solution: A comparison of NMR spin

relaxation measurements and molecular dynamics simulations. J. Mol. Biol. 246:356{365,

1995.

[110] Arfken, G. Mathematical methods for physicists. New York: Academic Press. 1970.

[111] Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., Gronenborn, A. M. Deviations

from the simple two-parameter model-free approach to the interpretation of nitrogen-15

nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112:4989{4991, 1990.

[112] Peng, J. W., Wagner, G. Mapping of spectral density functions using heteronuclear NMR

relaxation measurements. J. Magn. Reson. 98:308{332, 1992.

[113] Kalk, A., Berendsen, H. J. C. Proton magnetic relaxation and spin di�usion in proteins.

J. Magn. Reson. 24:343{366, 1976.

[114] Ernst, R. R., Bodenhausen, G., Wokaun, A. Principles of nuclear magnetic resonance in

one and two dimensions. Oxford: Clarendon Press. 1987.

[115] Torda, A. E., Scheek, R. M., van Gunsteren, W. F. Time-dependent distance restraints in

molecular dynamics simulations. Chem. Phys. Lett. 157:289{294, 1989.

136 BIBLIOGRAPHY

[116] Torda, A. E., Scheek, R. M., van Gunsteren, W. F. Time-averaged nuclear overhauser

e�ect distance restraints applied to tendamistat. J. Mol. Biol. 214:223{235, 1990.

[117] Kemmink, J., Scheek, R. M. Dynamic modelling of a helical peptide in solution using NMR

data: Multiple conformations and multi-spin e�ects. J. Biomol. NMR 6:33{40, 1995.

[118] Post, C. B. Internal motional averaging and three-dimensional structure determination by

nuclear magnetic resonance. J. Mol. Biol. 224:1087{1101, 1992.

[119] Br�uschweiler, R., Roux, B., Blackledge, M., Griesinger, C., Karplus, M., Ernst, R. R. In u-

ence of rapid intramolecular motion on NMR cross-relaxation rates. a molecular dynamics

study of antamanide in solution. J. Am. Chem. Soc. 114:2289{2302, 1992.

[120] Palmer III, A. G., Case, D. A. Molecular dynamics analysis of NMR relaxation in a

zinc-�nger peptide. J. Am. Chem. Soc. 114:9059{9067, 1992.

[121] Chandrasekhar, I., Clore, G. M., Szabo, A., Gronenborn, A. M., Brooks, B. R. A 500 ps

molecular dynamics simulation study of interleukin-1� in water. J. Mol. Biol. 226:239{250,

1992.

[122] Eriksson, M. A. L., Berglund, H., H�ard, T., Nilsson, L. A comparison of 15N NMR

relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the

glucocorticod receptor DNA-binding domain. PROTEINS: Struct. Funct. Gen. 17:375{390,

1993.

[123] Lipari, G., Szabo, A., Levy, R. M. Protein dynamics and NMR relaxation: comparison of

simulations with experiment. Nature 300:197{198, 1982.

[124] Olejniczak, E. T., Dobson, C. M., Karplus, M., Levy, R. M. Motional averaging of proton

nuclear overhauser e�ects in proteins. predictions from a molecular dynamics simulation

of lysozyme. J. Am. Chem. Soc. 106:1923{1930, 1984.

[125] Woody, R. W. Cicular dichroism. Methods in Enyzmology 246:34{70, 1995.

[126] Bayley, P. M., Nielsen, E. B., Schellman, J. A. The rotary properties of molecules containing

two peptide groups: Theory. J. Phys. Chem. 73:228{243, 1969.

[127] Manning, M. C., Woody, R. W. Theoretical study of the contribution of aromatic side

chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor. Biochemistry

28:8609{8613, 1989.

[128] Manning, M. C., Woody, R. W. Theoretical CD studies of polypeptide helices: Examina-

tion of important electronic and geometric factors. Biopolymers 31:569{586, 1991.

[129] Marconi, G., Monti, S., Mayer, B., K�ohler, G. Cicular dichroism of methylated phenols

included in �-cyclodextrin. an experimental and theoretical study. J. Phys. Chem. 99:3943{

3950, 1995.

[130] Fleischhauer, J., Groetzinger, J., Kramer, B., Krueger, P., Wollmer, A., Woody, R. W.,

Zobel, E. Calculation of the circular dichroism spectrum of cyclo(L-tyr-L-tyr) based on a

molecular dynamics simulation. Bioph. Chem. 49:141{152, 1994.

[131] Dehle, F. J., Finley, J. W., Stephens, P. J., Frisch, M. J. Ab initio calculation of vibrational

absorption and circular dichroism spectra using density functional force �elds: A compar-

ison of local, nonlocal, and hybrid density functionals. J. Phys. Chem. 99:16883{16902,

1995.

BIBLIOGRAPHY 137

[132] Hirst, J. D., Brooks III, C. L. Helicity, circular dichroism and molecular dynamics of

proteins. J. Mol. Biol. 243:173{178, 1994.

[133] van der Graaf, M., Hemminga, M. A. Conformational studies on a peptide representing

the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR

spectroscopy. Eur. J. Biochem. 201:489{494, 1991.

[134] Kungl, A. J., Breitenbach, M., Kau�mann, H. F. Molecular dynanamics simulation of the

rare amino acid LL-dityrosine and dityrosine-containing peptide: comparison with time

resolved uorescence. Biochim. Biophys. Acta 1201:345{352, 1994.

[135] Moore, P. B. Small-angle scattering. information content and error analysis. J. Appl.

Crystallogr. 168{175, 1980.

[136] Kataoka, M., Persechini, A., Tokunaga, F., Kretsinger, R. H. The linker of calmodulin

lacking Glu84 is elongated in solution, although it is bent in the crystal. PROTEINS:

Struct. Funct. Gen. 25:335{341, 1996.

[137] Hansen, J. P., McDonald, I. R. Theory of Simple Liquids. Second Ed. London, UK:

Academic Press. 1990.

[138] Zhu, S.-B., Singh, S., Robinson, G. W. Field-perturbed water. Adv. Chem. Phys. 85:627{

731, 1994.

[139] �Astrand, P. O., Wallqvist, A., Karlstr�om, G., Linse, P. Properties of urea-water solva-

tion calculated from a new ab initio polarizable intermolecular potential. J. Chem. Phys.

95:8419{8429, 1991.

[140] Boek, E. S., Briels, W. J., van Eerden, J., Feil, D. Molecular-dynamics simulations of

interfaces between water and crystalline urea. J. Chem. Phys. 96:7010, 1992.

[141] Boek, E. S., Briels, W. J. Molecular-dynamics simulations of aqueous urea solutions:

Study of dimer stability and solution structure and calculation of the total nitrogen radial

distribution function gn(r). J. Chem. Phys. 98:1422, 1993.

[142] Hern�andez-Cobos, J., Ortega-Blake, I., Bonilla-Mar��n, M., Moreno-Bello, M. A re�ned

monte carlo study of aqueous urea solutions. J. Chem. Phys. 99:9122{9134, 1993.

[143] Du�y, E. M., Severance, D. L., Jorgensen, W. L. Urea: Potential function, log P and free

energy of hydration. Isr. J. Chem. 33:323{330, 1993.

[144] Du�y, E. M., Kwalczyk, P. J., Jorgensen, W. L. Do denaturants interact with aromatica

hydrocarbons in water ? J. Am. Chem. Soc. 115:9271{9275, 1993.

[145] �Astrand, P. O., Wallqvist, A., Karlstr�om, G. Non-empirical potentials for urea-water

systems. J. Chem. Phys. 100:1262{1273, 1994.

[146] �Astrand, P. O., Wallqvist, A., Karlstr�om, G. Molecular dynamics simulations of 2M aque-

ous urea solution. J. Phys. Chem. 98:8224{8233, 1994.

[147] Pugliese, L., Pr�evost, M., Wodak, S. J. Unfolding simulations of the 85-102 �-hairpin of

barnase. J. Mol. Biol. 251:432{447, 1995.

[148] Brooks III, C. L., Case, D. A. Simulations of peptide conformational dynamics and ther-

modynamics. Chem. Rev. 93:2487{2502, 1993.

[149] Kemmink, J., Creighton, T. E. Local conformation of peptides representing the entire

sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J. Mol. Biol.

234:861{878, 1993.

138 BIBLIOGRAPHY

[150] van Mierlo, C. P. M., Darby, N. J., Neuhaus, D., Creighton, T. E. (14-38, 30-51)

double-disulphide intermediate in folding of bovine pancreatic trypsin inhibitor: A two-

dimensional 1H nuclear magnetic resonance study. J. Mol. Biol. 222:353{371, 1991.

[151] Worth, G. A., Wade, R. C. The aromatic-(i+2) amine interaction in peptides. J. Phys.

Chem. 99:17473{17482, 1995.

[152] Kemmink, J., Creighton, T. E. The physical properties of local interactions of tyrosine

residues in peptides and unfolded proteins. J. Mol. Biol. 245:251{260, 1995.

[153] Cheney, J., Cheney, B. V., Richards, W. G. Calculation of NH-� hydrogen bond energies

in basic pancreatic trypsin inhibitor. Biochim. Biophys. Acta 954:137{139, 1988.

[154] Mavri, J., Koller, J., Had�zi, D. Ab initio and AM1 calculations on model systems of

acetylcholine binding: complexes of tetramethylammonium with aromatics, neutral and

ionic formic acid. J. Mol. Struct. (THEOCHEM) 283:305{312, 1993.

[155] Mitchell, J. B. O., Nandi, C. L., McDonald, I. K., Thornton, J. M., Price, S. L.

Amino/aromatic interactions in proteins: Is the evidence stacked against hydrogen bond-

ing? J. Mol. Biol. 239:315{331, 1994.

[156] T�uchsen, E., Woodward, C. Assignment of asparagine-44 side-chain primary amide 1H

NMR resonance and the peptide amide N1H resonance of glycine-37 in basic pancreatic

trypsin inhibitor. Biochemistry 26:1918{1925, 1987.

[157] MSI. QUANTA 3.0. Molecular Simulations Incorporated York, United Kingdom 1994.

[158] Wlodawer, A., Nadchman, J., Gilliland, G. L., Gallagher, W., Woodward, C. Structure of

form III crystals of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 198:469{480, 1987.

[159] van Buuren, A. R., Marrink, S. J., Berendsen, H. J. C. A molecular dynamics study of the

decane/water interface. J. Phys. Chem. 97:9206{9212, 1993.

[160] Mark, A. E., van Helden, S. P., Smith, P. E., Janssen, L. H. M., van Gunsteren, W. F.

Convergence properties of free energy calculations: �-cyclodextrin complexes as a case

study. J. Am. Chem. Soc. 116:6293{6302, 1994.

[161] Daura, X., Oliva, B., Querol, E., Avil�es, F. X., Tapia, O. On the sensitivity of MD tra-

jectories to changes in water-protein interaction parameters: The potato carboxypeptidase

inhibitor in water as a test case for the GROMOS force �eld. PROTEINS: Struct. Funct.

Gen. 25:89{103, 1996.

[162] King, P. M., Mark, A. E., van Gunsteren, W. F. Re-parameterization of aromatic interac-

tions in the GROMOS force-�eld. Private Communication 1993.

[163] Jorgensen, W. L., Severance, D. L. Aromatic-aromatic interactions: Free energy pro�les for

the benzene dimer in water, chloroform and liquid benzene. J. Am. Chem. Soc. 112:4768{

4774, 1990.

[164] Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Hermans, J. Interaction

models for water in relation to protein hydration. In: Intermolecular Forces. Pullman, B.

ed. . D. Reidel Publishing Company Dordrecht 1981 331{342.

[165] Berendsen, H. J. C., Grigera, J. R., Straatsma, T. P. The missing term in e�ective pair

potentials. J. Phys. Chem. 91:6269{6271, 1987.

BIBLIOGRAPHY 139

[166] Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., Klein, M. L. Compar-

ison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926{935,

1983.

[167] B�aez, L. A., Clancy, P. Existence of a density maximum in extended simple point charge

water. J. Chem. Phys. 101:9837{9840, 1994.

[168] Berendsen, H. J. C., Postma, J. P. M., DiNola, A., Haak, J. R. Molecular dynamics with

coupling to an external bath. J. Chem. Phys. 81:3684{3690, 1984.

[169] Ryckaert, J. P., Ciccotti, G., Berendsen, H. J. C. Numerical integration of the cartesian

equations of motion of a system with constraints; molecular dynamics of n-alkanes. J.

Comp. Phys. 23:327{341, 1977.

[170] Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of

protein structures. J. Appl. Cryst. 24:946{950, 1991.

[171] Thornton, J. M. Protein structures: The end point of the folding pathway. In: Protein

Folding. Creighton, T. E. ed. . Freeman 1992 59{81.

[172] Burley, S. K., Petsko, G. A. Amino-aromatic interactions in proteins. J. Mol. Biol. 203:139{

143, 1986.

[173] Ahlstr�om, P., Wallqvist, A., Engstr�om, S., J�onsson, B. A molecular dynamics study of

polarizable water. Mol. Phys. 68:563{581, 1989.

[174] Cieplak, P., Kollman, P. A., Lybrand, T. A new water potential including polarization:

Application to gas-phase, liquid, and crystal properties of water. J. Chem. Phys. 92:6755{

6760, 1990.

[175] Caldwell, J., Dang, L. X., Kollman, P. A. Implementation of nonnadditive intermolecular

potentials by use of molecular dynamics: Development of a water-water potential and

water-ion cluster interactions. J. Am. Chem. Soc. 112:9144{9147, 1990.

[176] Jordan, P. C., van Maaren, P. J., Mavri, J., van der Spoel, D., Berendsen, H. J. C. Towards

phase transferable potential functions: Methodology and application to nitrogen. J. Chem.

Phys. 103:2272{2285, 1995.

[177] Axelsen, P. H., Gratton, E., Prendergast, F. G. Experimentally verifying molecular dynam-

ics simulations through uorescence anisotropy measurements. Biochemistry 30:1173{1179,

1991.

[178] Gordon, H. L., Jarrell, H. C., Szabo, A. G., Wills, K. J., Somorjai, R. L. Molecular

dynamics simulations of the conformational dynamics of tryptophan. J. Phys. Chem.

96:1915{1921, 1992.

[179] Hughes, J., Smith, T. W., Kosterlitz, H. W., Fothergill, L. A., Morgan, B. A., Morris,

H. R. Identi�cation of two related pentapeptides from the brain with potent opiate agonist

activity. Nature 258:577{579, 1975.

[180] Garbay-Jaureguiberry, C., Roques, B. P., Oberlin, R., Anteunis, M., Combrisson, S., Lalle-

mand, J. Y. 1H and 13C NMR studies of conformational behaviour of Leu-enkephalin.

FEBS Lett. 76:93{98, 1977.

[181] Stimson, E. R., Meinwald, Y. C., Scheraga, H. A. Solution conformation of enkephalin. a

nuclear magnetic resonance study of 13C-enriched carbonyl carbons in [Leu5]-enkephalin.

Biochemistry 18:1661{1671, 1979.

140 BIBLIOGRAPHY

[182] Higashijima, T., Kobayashi, J., Miyazawa, T. Nuclear magnetic resonance study on Met-

enkephalin and Met-enkephalinamide. Eur. J. Biochem. 97:43{57, 1979.

[183] Gupta, G., Sarma, M. H., Sarma, R. H., Dhingra, M. M. NOE data at 500 MHz reveal

the proximity of phenyl and tyrosine rings in enkephalin. FEBS Lett. 198:245{250, 1986.

[184] Motta, A., Picone, D., Tancredi, T., Temussi, P. A. NOE measurements on linear peptides

in cryoprotective aqueous mixtures. J. Magn. Reson. 75:364{370, 1987.

[185] Motta, A., Tancredi, T., Temussi, P. A. Nuclear overhauser e�ects in linear peptides.

FEBS Lett. 215:215{218, 1987.

[186] Gerothanassis, I. P., Karayannis, T., Sakarellis-Daitsiotis, M., Sakarellos, C., Marraud, M.

Nitrogen-14 nuclear magnetic resonance of the amino terminal group of Leu-enkephalin in

aqueous solution. J. Magn. Reson. 75:513{516, 1987.

[187] Motta, A., Picone, D., Tancredi, T., Temussi, P. A. Low temperature NMR studies of

Leu-enkephalins in cryoprotective solvents. Tetrahedron 44:975{990, 1988.

[188] Surewicz, W. K., Mantsch, H. H. Solution and membrane structure of enkephalins as

studied by infrared spectroscopy. Biochem. Biophys. Res. Comm. 150:245{251, 1988.

[189] Glasser, L., Scheraga, H. A. Calculations on crystal packing of a exible molecule, Leu-

enkephalin. J. Mol. Biol. 199:513{524, 1988.

[190] Sakarellos, C., Gerothanassis, I. P., Birlirakis, N., Karayannis, T., Sakarellos-Daitsiotis, M.17O-NMR studies of the conformational and dynamics properties of enkephalins in aqueous

and organic solutions using selective labeled analogues. Biopolymers 28:15{26, 1989.

[191] Vesterman, B., Saulitis, J., Betins, J., Liepins, E., Nikiforovich, G. V. Dynamic space

structure of the Leu-enkephalin molecule in DMSO solution. Biochim. Biophys. Acta

998:204{209, 1989.

[192] Picone, D., D'Ursi, A., Motta, A., Tancredi, T., Temussi, P. A. Conformational preferences

of [Leu5]enkephalin in biomimetic media. Eur. J. Biochem. 192:433{439, 1990.

[193] Moret, E., Gerothanassis, I. P., Hunston, R. N., Lauterwein, J. Does a 2 5 �-turn

structure exist in enkephalins? FEBS Lett. 262:173{175, 1990.

[194] Gerothanassis, I. P., Birlirakis, N., Karayannis, T., Tsikaris, V., Sakarellos-Daitsiotis, M.,

Sakarellos, C., Vitous, B., Marraud, M. 17O NMR and FT-IR study of the ionization state

of peptides in aprotic solvents. FEBS Lett. 298:188{190, 1992.

[195] Graham, W. H., Carter II, E. S., Hicks, R. P. Conformational analysis of Met-enkephalin

in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using

multidimensionl NMR and molecular modelling. Biopolymers 32:1755{1764, 1992.

[196] Doi, M., Ishibe, A., Shinozaki, H., Urata, H., Inoue, M., Ishida, T. Conserved and

novel structural characteristics of enantiomorphic Leu-enkephalin. Int. J. Pept. Prot. Res.

43:325{331, 1994.

[197] Smith, P. E., Pettitt, B. M. Peptides in ionic solutions: A comparison of the ewald and

switching function techniques. J. Chem. Phys. 95:8430{8441, 1991.

[198] Smith, P. E., Pettitt, B. M. E�ects of salt on the structure and dynamics of the

bis(penicillamine) enkaphalin zwitterion: A simulation study. J. Am. Chem. Soc. 113:6029{

6037, 1991.

BIBLIOGRAPHY 141

[199] Perez, J. J., Loew, G. H., Villar, H. O. Conformational study of met-enkephalin in its

zwitterionic form. Int. J. Quant. Chem. 44:263{275, 1992.

[200] Meirovitch, H., Meirovitch, E., Michel, A., V�asquez, M. A simple and e�ective procedure

for conformational search of macromolecules: Application to Met- and Leu-enkephalin. J.

Phys. Chem. 98:6241{6243, 1994.

[201] Zhorov, B. S., Ananthanarayanan, V. S. Similarity of Ca2+-bound conformations of mor-

phine and Met-enkephalin: a computational study. FEBS Lett. 354:131{134, 1994.

[202] de Loof, H., Nilsson, L., Rigler, R. Molecular dynamics simulations of galanin in aqueous

and nonaqueous solution. J. Am. Chem. Soc. 114:4028{4035, 1992.

[203] Brooks III, C. L., Nilsson, L. Promotion of helix formation in peptides dissolved in alcohol

and water-alcohol mixtures. J. Am. Chem. Soc. 115:11034{11035, 1993.

[204] Bodkin, M. J., Goodfellow, J. M. Hydrophobic solvation in aqueous tri uoroethanol solu-

tion. Biopolymers 39:43{50, 1996.

[205] Mierke, D. F., Kessler, H. Molecular dynamics with dimethyl sulfoxide as a solvent. con-

formation of a cyclic hexapeptide. J. Am. Chem. Soc. 113:9446, 1991.

[206] Mierke, D. F., Kessler, H. Improved molecular dynamics simulations for the determination

of peptide structures. Biopolymers 33:1003{1017, 1993.

[207] Chandler, D. Statistical mechanics of isomerization dynamics in liquids and the transition

state approximation. J. Chem. Phys. 68:2959{2970, 1978.

[208] Zhang, Y., Pastor, R. W. A comparison of methods for computing transition rates from

molecular dynamics simulation. Mol. Sim. 13:25{38, 1994.

[209] Liu, H., M�uller-Plathe, F., van Gunsteren, W. F. A force �eld for liquid dimethyl sulfoxide

and liquid proporties of liquid dimethyl sulfoxide calculated using molecular dynamics

simulation. J. Am. Chem. Soc. 117:4363{4366, 1995.

[210] Miyamoto, S., Kollman, P. A. SETTLE: An analytical version of the SHAKE and RATTLE

algorithms for rigid water models. J. Comp. Chem. 13:952{962, 1992.

[211] Dyson, H. J., Wright, P. E. De�ning solution conformations of small linear peptides. Annu.

Rev. Biophys. Biophys. Chem. 20:519{538, 1991.

[212] Dyson, H. J., Wright, P. E. Peptide conformation and protein folding. Curr. Opin. Struct.

Biol. 3:60{65, 1993.

[213] Hermans, J. Molecular dynamics simulations of helix and turn propensities in model

peptides. Curr. Opin. Struct. Biol. 3:270{276, 1993.

[214] Tobias, D. J., Mertz, J. E., Brooks III, C. L. Nanosecond timescale folding dynamics of a

pentapaptide in water. Biochemistry 30:6054{6058, 1991.

[215] Dasgupta, R., Kaesberg, P. Complete nucleotide sequence of the coat protein messenger

RNAs of brome mosaic virus and cowpea chlorotic mottle virus. Nucl. Acid. Res. 10:703{

713, 1982.

[216] Bancroft, J. B., Hiebert, E. Formation of an infectious nucleoprotein from protein and

nucleic acid isolated from a small spherical virus. Virology 32:354{356, 1967.

142 BIBLIOGRAPHY

[217] Vriend, G., Hemminga, M. A., Verduin, B. J. M., de Wit, J. L., Schaafsma, T. J. Segmental

mobility involved in protein-RNA interaction in cowpea chlorotic mottle virus. FEBS Lett.

134:167{171, 1981.

[218] Vriend, G., Verduin, B. J. M., Hemminga, M. A., Schaafsma, T. J. Mobility involved in

protein-RNA interaction in spherical plant viruses, studied by nuclear magnetic resonance

spectroscopy. FEBS Lett. 145:49{52, 1982.

[219] Vriend, G., Verduin, B. J. M., Hemminga, M. A. Role of the N-terminal part of the coat

protein in the assembly of cowpea chlorotic mottle virus. J. Mol. Biol. 191:453{460, 1986.

[220] ten Kortenaar, P. B. W., Kr�use, J., Hemminga, M. A., Tesser, G. I. Synthesis of an arginine

rich fragment of a viral coat protein using guanidium functions exclusively. Int. J. Pept.

Prot. Res. 27:401{413, 1986.

[221] van der Graaf, M., Kroon, G. J. A., Hemminga, M. A. Conformation and mobility of the

RNA-binding N-terminal part of the intact coat protein of cowpea chlorotic mottle virus.

A two dimensional Nuclear Magnetice Resonance study. J. Mol. Biol. 220:701{709, 1991.

[222] van der Graaf, M., Scheek, R. M., van der Linden, C. C., Hemminga, M. A. Conformation

of a pentacosapeptide representing the RNA-binding N-terminus of cowpea chlorotic mottle

virus coat protein in the presence of oligophosphates: A two-dimensional proton Nuclear

Magnetic Resonance and distance geometry study. Biochemistry 31:9177{9182, 1992.

[223] Timashe�, S. N. Solvent e�ects on protein stability. Curr. Opin. Struct. Biol. 2:35{39,

1992.

[224] Sijpkes, A. H., van der Kleut, G., Gill, S. C. Urea-diketopiperazine interactions: A model

for urea induced denaturation of proteins. Bioph. Chem. 46:171, 1993.

[225] Kovacs, H., Mark, A. E., Johansson, J., van Gunsteren, W. F. The e�ect of environment on

the stability of an integral membrane helix: Molecular dynamics simulations of surfactant

protein C in chloroform, methanol and water. J. Mol. Biol. 247:808{822, 1995.

[226] Smith, P. E., Marlow, G. E., Pettitt, B. M. Peptides in ionic solutions: A simulation

study of a bis(penicillamine) enkaphalin in sodium acetate solution. J. Am. Chem. Soc.

115:7493{7498, 1993.

[227] van Schaik, R. C., Berendsen, H. J. C., Torda, A. E., van Gunsteren, W. F. A structure

re�nement method based on molecular dynamics in 4 spatial dimensions. J. Mol. Biol.

234:751{762, 1993.

[228] Clarage, J. B., Philips Jr, G. N. Cross-validation tests of time-averaged molecular dynamics

re�nements for determination of protein structures by X-ray crystallography. Act. Cryst.

D. 50:24{36, 1994.

[229] Fennen, J., Torda, A. E., van Gunsteren, W. F. Structure re�nement with molecular

dynamics and Boltzmann-weighted ensemble. J. Biomol. NMR 6:163{170, 1995.

[230] Frisch, M. J., Trucks, G. W., Schlegel, H. B., Gill, P. M. W., Johnson, B. G., Wong, M. W.,

Foresman, J. B., Robb, M. A., Head-Gordon, M., Replogle, E. S., Gomperts, R., Andres,

J. L., Raghavachari, K., Binkley, J. S., Gonzalez, C., Martin, R. L., Fox, D. J., Defrees,

D. J., Baker, J., Stewart, J. J. P., Pople, J. A. Gaussian 92/DFT, revision G. 1. Gaussian,

Inc. Pittsburgh PA 1993.

BIBLIOGRAPHY 143

[231] Lee, W. K., Prohofsky, E. W. A molecular dynamics study of the solvation of a sodium

ion bound to dihydrogen phosphate ion. Chem. Phys. Lett. 85:98{102, 1982.

[232] �Osapay, K., Case, D. A. Analysis of proton chemical shifts in regular secondary structure

of proteins. J. Biomol. NMR 4:215{230, 1994.

[233] Berendsen, H. J. C. Electrostatic interactions. In: Computer Simulation of Biomolecular

Systems. van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J. eds. . ESCOM Leiden

1993 161{181.

[234] Speir, J. A., Munshi, S., Wang, G., Baker, T. S., Johnson, J. E. Structures of the native

and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography

and cryo-electron microscopy. Structure 3:63{78, 1995.

[235] van der Graaf, M. Conformation of the RNA-binding N-terminus of the coat protein of cow-

pea chlorotic mottle virus. PhD thesis. Wageningen Agricultural University. Wageningen,

The Netherlands. 1992.

[236] Hockney, R. W., Eastwood, J. W. Computer simulation using particles. New York:

McGraw-Hill. 1981.

[237] Luty, B. A., Davies, M. E., Tironi, I. G., van Gunsteren, W. F. A comparison of particle-

particle, particle-mesh and ewald methods for calculating electrostatic interactions in pe-

riodic molecular systems. Mol. Sim. 14:11{20, 1994.

[238] DiCapua, F. M., Swaminathan, S., Beveridge, D. L. Theoretical evidence for destabilization

of an � helix by water insertion: Molecular dynamics of hydrated decaalanine. J. Am.

Chem. Soc. 112:6768{6771, 1990.

[239] Kim, P. S., Baldwin, R. L. Intermediates in the folding reactions of small proteins. Annu.

Rev. Biochem. 60:631{660, 1990.

[240] Roder, H., El�ove, G. A., Englander, S. W. Structural characterization of folding inter-

mediates in cytochrome c by H-exchange labeling and proton NMR. Nature 335:700{704,

1988.

[241] Udgaonkar, J. B., Baldwin, R. L. NMR evidence for an early framework intermediate on

the folding pathway of ribonuclease A. Nature 335:694{699, 1988.

[242] Englander, S. W., Mayne, L. Protein folding studied using hydrogen-exchange labeling

and two-dimensional NMR. Annu. Rev. Biophys. 21:243{265, 1992.

[243] Shin, H.-C., Merutka, G., Waltho, J. P., Tennant, L. L., Dyson, H. J., Wright, P. E.

Peptide models of protein folding initiation sites. 3. the G-H helical hairpin of myoglobin.

Biochemistry 32:6356{6364, 1993.

[244] Tsou, C.-L. Folding of the nascent peptide chain into a biologically active protein. Bio-

chemistry 27:1807{1812, 1988.

[245] Fedorov, A. N., Friguet, B., Djavadi-Ohaniance, L., Alakhov, Y. B., Goldberg, M. E.

Folding on the ribosome of Escherichia coli tryptophan synthase � subunit nascent chains

probed with a conformation-dependent monoclonal antibody. J. Mol. Biol. 228:351{358,

1992.

[246] Hata-Tamaka, A., Kawai, G., Yamasaki, K., Ito, Y., Kajiura, H., Ha, J.-M., Miyazawa,

T., Yokoyama, S., Nishimura, S. Spin-labeling proton NMR study on aromatic amino

acid residues in the guanine nucleotide binding site of human c-Ha-ras(1-171) protein.

Biochemistry 28:9550{9556, 1989.

144 BIBLIOGRAPHY

[247] Minara, P., Hall, L., Betton, J.-M., Missiakis, D., Yon, J. M. E�cient expression and

characterization of isolated structural domains of yeast phosphateglycerate kinase genrated

by site-directed mutagenesis. Prot. Eng. 3:55{60, 1989.

[248] Eder, J., Kirschner, K. Stable substructures of eightfold ��-barrel proteins: Fragment

complementation of phosphoribosylanthranilate isomerase. Biochemistry 31:3617{3625,

1992.

[249] Jecht, M., Tomschy, A., Kirschner, K., Jaenicke, R. Autonomous folding of the excised

coenzyme-binding domain of an D-glyceraldehyde 3-phosphate dehydrogenase from ther-

motoga maritima. Prot. Sci. 3:411{418, 1994.

[250] Schulz, G. E. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2:61{67, 1992.

[251] Baker, P. J., Britton, K. L., Rice, D. W., Stillman, A. R. T. J. Structural consequences

of sequence patterns in the �ngerprint region of the nucleotide binding fold. J. Mol. Biol.

228:662{671, 1992.

[252] Saraste, M., Sibbald, P. R., Wittinghofer, A. The P-loop - a common motif in ATP and

GTP binding proteins. Trends Biochem. Sci. 15:430{434, 1990.

[253] Bossemeyer, D. The glycine-rich sequence of protein kinases: a multifunctional element.

Trends Biochem. Sci. 19:201{205, 1994.

[254] Wierenga, R. K., Terpstra, P., Hol, W. G. J. Prediction of the occurence of the ADP-

binding ���-fold in proteins, using an amino acid sequence �ngerprint. J. Mol. Biol.

187:101{107, 1986.

[255] Krasheninnikov, I. A., Komar, A. A., Adzhubei, I. A. Frequencies of utilization of codons in

mRNA and coding of the domain structure of proteins. Dokl. Akad. Nauk. SSSR 305:1006{

1012, 1989.

[256] Opitz, U., Rudolph, R., Jaenicke, R., Ericsson, L., Neurath, H. Proteolytic dimers of

porcine muscle lactate dehydrogenase: Characterisation, folding, and reconstitution of the

truncated and nicked polypeptide chain. Biochemistry 26:1399{1406, 1987.

[257] Rossmann, M. G., Moras, D., Olsen, K. W. Chemical and biological evolution of a

nucleotide-binding protein. Nature 250:194{199, 1974.

[258] Daggett, V., Levitt, M. Realistic simulations of native-protein dynamics. Annu. Rev.

Biophys. Biomol. Struct. 22:353{380, 1993.

[259] Soman, K. V., Karimi, A., Case, D. A. Molecular dynamics analysis of a ribonuclease

C-peptide analogue. Biopolymers 33:1567{1580, 1993.

[260] Braxenthaler, M., Avbelj, F., Moult, J. Structure, dynamics and energetics of initiation

sites in protein folding: I. Analysis of a 1 ns molecular dynamics trajectory of an early

folding unit in water: The helix I/loop I-fragment of barnase. J. Mol. Biol. 250:239{257,

1995.

[261] Hinds, D. A., Levitt, M. Simulation of protein-folding pathways: lost in (conformational)

space. Trends Biotech. 13:23{27, 1995.

[262] Abad-Zapatero, C., Gri�th, J. P., Sussman, J. L., Rossmann, M. G. Re�ned crystal

structure of M4 dog�sh apo-lactate dehydrogenase. J. Mol. Biol. 198:445{467, 1987.

[263] Tironi, I. G., Sperb, R., Smith, P. E., van Gunsteren, W. F. A generalized reaction �eld

method for molecular dynamics simulations. J. Chem. Phys. 102:5451{5459, 1995.

BIBLIOGRAPHY 145

[264] Luty, B. A., van Gunsteren, W. F. Calculating electrostatic interactions using the particle-

particle, particle-mesh method with non-periodic long-range interactions. J. Phys. Chem.

[265] van der Spoel, D., Berendsen, H. J. C., van Buuren, A. R., Apol, E., Meulenho�, P. J.,

Sijbers, A. L. T. M., van Drunen, R. Gromacs User Manual. Nijenborgh 4, 9747 AG

Groningen, The Netherlands. Internet: http://rugmd0.chem.rug.nl/�gmx 1995.

[266] Das, B., Chattopadhyay, S., Gupta, C. D. Reactivation of denatured fungal glucose 6-

phosphate dehydrogenase and E. coli alkaline phosphatase with E. coli ribosome. Biochem.

Biophys. Res. Comm. 183:774{780, 1992.

[267] Bera, A. K., Das, B., Chattapahyay, S., Dasgupta, C. Refolding of denatured restric-

tion endonucleases with ribosomal preparations from methanosarcina barkeri. Biochem.

Biophys. Res. Comm. 32:315{323, 1994.

[268] Girg, R., Jaenicke, R., Rudolph, R. Dimers of porcine skeletal muscle lactate dehydroge-

nase produced by limited proteolysis during reassociation are enzymatically active in the

presence of stabilizing salt. Bioch. Int. 7:433{441, 1983.

[269] Blanco, F. J., Jimenez, M. A., Herranz, J., Rico, M., Santoro, J., Nieto, J. L. NMR

evidence of a short linear peptide that folds into a �-hairpin in aqueous solution. J. Am.

Chem. Soc. 115:5887{5888, 1993.

[270] Blanco, F. J., Jimenez, M. A., Pineda, A., Rico, M., Santoro, J., Nieto, J. L. NMR

solution structure of the isolated N-terminal fragment of protein-G B1 domain; evidence

of tri uoroethanol induced native-like �-hairpin formation. Biochemistry 33:6004{6014,

1994.

[271] Wierenga, R. K., de Maeyer, M. C. H., Hol, W. G. J. Interaction of phosphate moieties

with �-helices in dinucleotide binding proteins. Biochemistry 24:1346{1357, 1985.

[272] Stroup, A. N., Gierasch, L. M. Reduced tendency to form a � turn in peptides from the

P22 tailspike protein correlates with a temperature-sensitive folding defect. Biochemistry

29:9765{9771, 1990.

[273] Fry, D. C., Kuby, S. A., Mildvan, A. S. NMR studies of the MgATP binding site of adenylate

kinase and of a 45-residue peptide fragment of the enzyme. Biochemistry 24:4630{4694,

1985.

[274] Fry, D. C., Byler, D. M., Susi, H., Brown, E. M., Kuby, S. A., Mildvan, A. S. Solution

structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by

2D-NMR, FTIR, and CD spectroscopy. Biochemistry 27:3588{3598, 1988.

[275] Tobias, D. J., Sneddon, S. F., Brooks III, C. L. Stability of a model �-sheet in water. J.

Mol. Biol. 227:1244{1252, 1992.

[276] Dobson, C. M., Evans, P. A., Radford, S. E. Understanding how proteins fold: The

lysozyme story so far. Trends Biochem. Sci. 19:31{37, 1994.

[277] Tweedy, N. B., Hurle, M. R., Chrunyk, B. A., Matthews, C. R. Multiple replacements

at position 211 in the � subunit of tryptophan synthase as a probe of the folding unit

association reaction. Biochemistry 29:1539{1545, 1990.

[278] Schafmeister, C. E., Miercke, L. J. W., Stroud, R. M. Structure at 2.5 �A of a designed

peptide that maintains solubility of membrane proteins. Science 262:734{738, 1993.

146 BIBLIOGRAPHY

[279] Monera, O. D., Kay, C. M., Hodges, R. S. Electrostatic interactions control the paral-

lel and antiparallel orientation of �-helical chains in two stranded �-helical coiled coils.

Biochemistry 33:3862{3871, 1994.

[280] Alexandrov, N. Structural arguments for N-terminal initiation of protein folding. Prot.

Sci. 2:1989{1991, 1993.

[281] Finn, B. E., Fors�en, S. The evolving model of calmodulin structure, function and activation.

Structure 3:7{11, 1995.

[282] Ikura, M. Calcium binding and conformational response in EF-hand proteins. Trends

Biotech. 21:14{17, 1996.

[283] Vogel, H. J., Zhang, M. Protein engineering and NMR studies of calmodulin. Mol. Cell.

Bioch. 149/150:3{15, 1995.

[284] Zhang, M., Vogel, H. J. Two dimensional NMR studies of selenomethionine calmodulin.

J. Mol. Biol. 234:545{554, 1994.

[285] Vogel, H. J. Calmodulin: a versatile calcium mediator protein. Biochem. Cell. Biol.

72:357{376, 1994.

[286] Persechini, A., Kretsinger, R. H. The central helix of calmodulin functions as a exible

tether. J. Biol. Chem. 263:12175{12178, 1988.

[287] Spera, S., Ikura, M., Bax, A. Measurements of the exchange rates of rapidly exchanging

amide protons: Application to the study of calmodulin and its complex with a myosin light

chain kinase fragment. J. Biomol. NMR 1:155{165, 1991.

[288] Barbato, G., Ikura, M., Kay, L. E., Pastor, R. W., Bax, A. Backbone dynamics of calmod-

ulin studied by 15N relaxation using inverse detected NMR spectroscopy: The central helix

is exible. Biochemistry 31:5269{5278, 1992.

[289] Zhang, M., Tanaka, T., Ikura, M. Calcium-induced conformational transition revealed by

the solution structure of apo calmodulin. Nature Struct. Biol. 2:758{767, 1995.

[290] Tjandra, N., Kuboniwa, H., Ren, H., Bax, A. Rotational dynamics of calcium-free calmod-

ulin studied by 15N-NMR relaxation measurements. Eur. J. Biochem. 230:1014{1024, 1995.

[291] Kuboniwa, H., Tjandra, N., Grzesiek, S., Ren, H., Klee, C. B., Bax, A. Solution structure

of calcium-free calmodulin. Nature Struct. Biol. 2:768{776, 1995.

[292] Meador, W. E., Means, A. R., Quiocho, F. A. Target enzyme recognition by calmodulin:

2.4 �Angstr�om structure of a calmodulin-peptide complex. Science 257:1251, 1992.

[293] Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B., Bax, A. Solution struc-

ture of a calmodulin-target peptide complex by multidimensional NMR. Science 256:632,

1992.

[294] Clore, G. M., Bax, A., Ikura, M., Gronenborn, A. M. Structure of calmodulin-target

peptide complexes. Curr. Opin. Struct. Biol. 3:838{845, 1993.

[295] Mehler, E. L., Pascual-Ahuir, J. L., Weinstein, H. Structural dynamics of calmodulin and

troponin C. Prot. Eng. 4:625{637, 1991.

[296] Vorherr, T., Kessler, O., Mark, A., Carafoli, E. Construction and molecular dynamics

simulation of calmodulin in the extended and in a bent conformation. Eur. J. Biochem.

204:931{937, 1992.

BIBLIOGRAPHY 147

[297] Soman, K. V., Karimi, A., Case, D. A. Unfolding of an �-helix in water. Biopolymers

31:1351{1361, 1991.

[298] Levitt, M., Sander, C., Stern, P. S. The normal modes of a protein: Native bovine pancre-

atic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 10:181{199, 1983.

[299] G�o, N., Noguti, T., Nishikawa, T. Dynamics of a small globular protein in terms of low-

frequency vibrational modes. Proc. Natl. Acad. Sci. USA 80:3696{3700, 1983.

[300] Brooks, B., Karplus, M. Harmonic dynamics of proteins: Normal modes and uctuations

in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 80:6571{6575, 1983.

[301] Amadei, A., Linssen, A. B. M., Berendsen, H. J. C. Essential dynamics of proteins.

PROTEINS: Struct. Funct. Gen. 17:412{425, 1993.

[302] Vriend, G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph.

8:52{56, 1990.

[303] Kitao, A., Hirata, F., G�o, N. The e�ects of solvent on the conformation and the collective

motions of protein: normal mode analysis and molecular dynamics simulations of mellitin

in water and in vacuum. Chem. Phys. 158:447{472, 1991.

[304] Case, D. A. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:285{290,

1994.

[305] Garcia, A. E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696{

2699, 1992.

[306] Hayward, S., Kitao, A., Hirata, F., G�o, N. E�ect of solvent on collective motions in globular

proteins. J. Mol. Biol. 234:1207{1217, 1993.

[307] van Aalten, D. M. F., Amadei, A., Linssen, A. B. M., Eijsink, V. G. H., Berendsen, H.

J. C. The essential dynamics of thermolysin: Con�rmation of the hinge-bending motion

and comparison of simulations in vacuum and water. PROTEINS: Struct. Funct. Gen.

22:45{54, 1995.

[308] Bayley, P. M., Martin, S. R. The �-helical content of calmodulin is increased by solution

conditions favouring protein crystallisation. Biochim. Biophys. Acta 1160:16{21, 1992.

[309] Chattopadhyaya, R., Meador, W. E., Means, A. R., Quiocho, F. A. Calmodulin structure

re�ned at 1.7�A resolution. J. Mol. Biol. 228:1177, 1992.

[310] Weinstein, H., Mehler, E. L. Ca2+-binding and structural dynamics in the functions of

calmodulin. Annu. Rev. Physiol. 56:213{236, 1994.

[311] Chakrabartty, A., Baldwin, R. L. Stability of �-helices. Adv. Prot. Chem. 46:141{176,

1995.

[312] T�or�ok, K., Lane, A. N., Martin, S. R., Janot, J. M., Bayley, P. M. E�ects of calcium

binding on the internal dynamics properties of bovine brain calmodulin studied by NMR

and optical spectroscopy. Biochemistry 31:3452{3462, 1992.

[313] Terwilliger, T. C., Eisenberg, D. The structure of melittin. I. Structure determination and

partial re�nement. J. Biol. Chem. 257:6010{6015, 1982.

[314] Balsera, M. A., Wriggers, W., Oono, Y., Schulten, K. Principle component analysis and

long time protein dynamics. J. Phys. Chem. 100:2567{2572, 1996.

148 BIBLIOGRAPHY

[315] Basu, G., Kitao, A., Hirata, F., G�o, N. A collective motion description of the 310/�-helix

transition: Implications for a natural reaction coordinate. J. Am. Chem. Soc. 116:6307{

6315, 1994.

[316] Amadei, A., Linssen, A. B. M., de Groot, B. L., Aalten, D. M. F., Berendsen, H. J. C. An

e�cient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn.

13:615{626, 1996.

[317] de Groot, B. L., Amadei, A., Aalten, D. M. F., Berendsen, H. J. C. Towards an exhaustive

sampling of the con�gurational spaces of the two forms of the peptide hormone guanylin.

J. Biomol. Struct. Dyn. 13:741{752, 1996.

[318] van der Spoel, D., Berendsen, H. J. C. Determination of proton transfer rate constants

using ab initio, molecular dynamics and density matrix evolution calculations. In: Paci�c

Symposium on Biocomputing 1996. Hunter, L., Klein, T. eds. . World Scienti�c Singapore

1995 634{648.

[319] Scheek, R. M., Torda, A. E., Kemmink, J., van Gunsteren, W. F. Structure determination

by NMR: the modeling of NMR parameters as ensemble averages. In: Computational

Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance. Hoch,

J., Poulsen, F. M., Red�eld, C. eds. . Plenum Press New York 1991 209{217.