motifs of protein structures branden & tooze, chapter 2

Motifs of Protein Structures

Branden & Tooze, Chapter 2

Central Dogma of Molecular BiologyCentral Dogma of Molecular Biology

DNA RNA

protein

Transcription

Translationin ribosome

Protein Sequence to Structure

The primary structure is the sequence of AAs. Once formed, the sequences form secondary and tertiary structures, and sometimes quaternary structures, that are critical to their functions.

1° 2°

4° 3°

Proteins 1° Structure: The Sequence of Amino Proteins 1° Structure: The Sequence of Amino AcidsAcids

• Primary (1°): Sequence of amino acids– Primary structure held together by peptide bonds– Protein sequence determined by sequence of a gene in the genetic code– Determines 3D structure

http://protein-pdb.com/2011/10/04/primary-protein-structure/

Protein 2° StructureProtein 2° Structure

Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

Protein 2° Structure: The Protein 2° Structure: The αα-helix-helix• In globular proteins, may vary in length from 4-40 residues

• AA’s in an α helix arranged in a right-handed helix

• Each amino acid residue is rotated 100° relative to previous residue in helix– Helix has 3.6 residues per turn– H-bonds form between N-H groups at residue n and C=O groups at n+4

http://simplygeology.wordpress.com/tag/s-waves/

Helices – 3 Major TypesHelices – 3 Major Types

http://www.cryst.bbk.ac.uk/PPS2/course/section8/ss-960531_5.html

331010 Helix Helix

• 3 residues per turn and 10 atoms between H-bond donor and acceptor (n to n+3)

• Occurs rarely, and usually at end of α helix or as single turn helix

• Not energetically favorable since backbone atoms packed too tightly

ππ Helix Helix

• H-bonding occurs between residues n to n+5• Occurs rarely, and usually at end of α helix or as

single turn helix• Not energetically favorable since backbone

atoms packed too loosely (hole in the middle)

αα Helix has dipole moment Helix has dipole moment

• All N-H to C=O H-bonds go in the same direction, so there is a net pull of electron density towards the C-terminal end of the helix.

• Negatively charged ligands (e.g., phosphate groups) may bind to positively-charged N-terminal end, but the reverse is less likely to be observed.

N-terminal C-terminal

δ-δ+

Protein 2° Structure: Protein 2° Structure: αα Helices Helices

• Some residues more likely to be in helices than others:• Good helix formers: Met (M), Glu (E), Ala (A), Leu (L)• Poor helix formers: Gly (G), Pro (P), Ser (S), Tyr (Y)

• Helices tend to be on outside of protein, or have polar ends on the outside (hydrophilicity)

• Side chains tend to change from hydrophobic to hydrophilic every 3-4 residues

• Hydrophobic and hydrophilic residues tend to aggregate on opposite sides of the helix (see helical wheel below).

Proteins 2° Structure: The Proteins 2° Structure: The ββ-sheet-sheet• Beta (β) sheets (or pleated sheets) formed by H-bond connected

strands• β strands are like elongated helices without helical H-bonds

– Usually 5-10 residues long

• β Sheets may be parallel or antiparallel

http://www.chembio.uoguelph.ca/educmat/phy456/456lec01.htm

Proteins 2° Structure: Random Coils and LoopsProteins 2° Structure: Random Coils and Loops• Proteins typically contain regions lacking either sheet or helical

structures.– These are called Random Coils or Loops– Usually found at surface of protein (with charged and/or polar residues)

• Loops may perform important structural and functional roles, including:

– Connecting β strands form antiparallel sheets (hairpin loops or reverse turns)– Increasing flexibility (hinge motion)– Binding metal ions or other biomolecules to alter protein function

http://www.chembio.uoguelph.ca/educmat/phy456/456lec01.htm

Proteins 3° StructureProteins 3° Structure• Protein function determined by 3D shape• Tertiary structure results from residue interactions:

– H-bonding– Disulfide Bridges– Salt Bridges– Hydrophobic Interactions

Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

Proteins 3° StructureProteins 3° Structure• Polar and charged residues tend to be on surface of protein, exposed

to water, while hydrophobic residues tend to be buried

Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

Proteins 4° StructureProteins 4° Structure

• Functional proteins may contain two or more polypeptide chains held together by the same forces that control 3° structure:

– H-bonding– Disulfide Bridges– Salt Bridges– Hydrophobic Interactions

• Each chain is a subunit of structure

• Each subunit has its own 1°, 2° and 3° structure

Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

John Kendrew, 1958,

upon determining the molecular

structure of myoglobin:

“Perhaps the most remarkable features of the molecule are its complexity and

its lack of symmetry.

The arrangement seems to be almost totally lacking in the kind of regularities which one instinctively anticipates,

and it is more complicated than has been predicted by any theory of protein structure.”

Tertiary StructureTertiary structure describes how the secondary structure units associate within a single polypeptide chain to give a three-dimensional structure.

Quaternary structure describes how two or more polypeptide chains associate to form a native protein structure (but some proteins consist of a single chain).

Tertiary structures can be divided into three main classes:

domain domains domains

Proteins are Large MacromoleculesProteins are Large Macromolecules• Proteins are extremely large

– MW of glucose is 180 u, compared with 65,000 u for hemoglobin

• Proteins synthesized inside cells remain inside cells– The presence of intracellular proteins in blood or urine can be used to test for certain

diseases

Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

Protein FunctionsProtein Functions• Catalytic Function:

– Enzymes are proteins that catalyze biological functions

• Structural function:– Most human structural materials (excluding bone) are comprised of proteins– Collagen (bundled helices)

• 25-35% of total protein in body• Tendons• ligaments • Skin• Cornea• Cartilage• Bone• blood vessels• gut

– Keratin (bundled helices)• Chief constituent of hair, skin, fingernails

http://www.imb-jena.de/~rake/Bioinformatics_WEB/proteins_classification.html

Protein FunctionsProtein Functions• Storage Function:

– Storage of small molecules or ions– Ovalbumin

• Main protein in egg whites• Can be broken down into amino acids for use by developing embryos

– Ferritin• Globular complex of 24 protein subunits• Buffers iron concentration in cells

http://www.stagleys.demon.co.uk/explorers/genesandproteins/page6.html; http://ferritin.blogspot.com/

Ovalbumin (chicken egg white) ferritin

Protein FunctionsProtein Functions• Protective Function:

– Protection against external foreign substances

• Antibodies– Very large proteins

– Combine with, and destroy viruses, bacteria

Harris, L. J., Larson, S. B., Hasel, K. W., Day, J., Greenwood, A., McPherson, A. Nature 1992, 360, 369-372; http://courses.washington.edu/conj/immune/antibody.htm; http://www.colorado.edu/intphys/Class/IPHY3430-200/014blood.htm

Immunoglobulin

– blood clotting/Coagulation• thrombin

– Protease responsible for platelet aggregation and formation of fibrin

Protein FunctionsProtein Functions• Regulatory Function:

– Protein hormones• Insulin

– Protein hormone that directs cells in the liver, muscle, and fat to take up glucose from the blood and store it as glycogen

– Forms hexamer bound together by Zn

http://en.wikipedia.org/wiki/File:InsulinHexamer.jpg; Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7th Edition, 2011

Insulin

Protein FunctionsProtein Functions• Nerve impulse transmission:

– Rhodopsin• Protein found in rods cells of eye retina

– Converts light events into nerve impulses sent to the brain

http://cherfan2010biology12assessment.wikispaces.com/The+Retina

Protein FunctionsProtein Functions• Movement function:

– Proteins involved in muscle contraction• Myosin• Actin

http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/structural-proteins/actin.html

Protein FunctionsProtein Functions• Transport function:

– Transport ions or molecules throughout the body• Serum albumin: Transports fatty acids between fat and other tissues

• Hemoglobin: Transports O2 from lungs to other tissues (e.g., muscles)

• Transferrin: Transports iron in blood plasma

http://en.wikipedia.org/ ; http://www.pdb.org/pdb/101/motm.do?momID=37

Serum albumin hemoglobin

transferrin

Many Proteins Contain Intrinsic Metal Atoms

• (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules.

• (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains.

Ca2+-binding Calmodulin

(3cln)

Ca2+-free Calmodulin (1cfc)

Triggering

Calbindin D9K

(1b1g)

Thermolysin

(1tlx)

Buffering

Stabilizing

Calcium-binding proteins Calcium-binding proteins (CaBPs)(CaBPs)

Ca10-3

10-4

10-5

10-7

10-8

10-9

Kd (M)

α-Lactalbumin

Calmodulin

Thermolysin

Calbindin D9k

Parvalbumin

Protease K

CaR

Binding affinities

Assembly/Folding

Cocksfoot mottle virus capsid (1ng0)

Protein ClassificationsProtein Classifications

• Fibrous Proteins– Comprised of long stringlike molecules that can wrap around each other to form fibers– Usually insoluble in water– Major components of connective tissues (e.g., collagen, keratin)

• Globular proteins– Spherical– Usually water soluble– May be moved through the body (e.g., hemoglobin, transferrin)

http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/structural-proteins/actin.html

Based on structural shape

Based on composition• Simple Proteins

– Contain only amino acid residues

• Conjugated Proteins– Contain amino acid residues and other organic or inorganic components (i.e., prosthetic

groups)• Lipoproteins• Glycoproteins• metalloproteins

Folds of ProteinsFolds of Proteins

Helix, strand

Motifs

Folds/ Domain

Domains

Super Secondary Structures (Motifs)• Simple combinations of a few secondary structural

elements with a specific geometric arrangement are called super secondary structures or motifs.

• They may have functional and structural significance.

• Individual motifs may not be stable folding units. They may require association with other motifs.

• Common motifs: Helix-turn-helix -hairpin, -meander-barrel, Geek key

Helix-Turn-Helix Motif

• Two helices that are connected by a short loop region in a specific geometric arrangement constitute a helix-turn-helix motif. (a) the DNA-binding motif and (b) the calcium-binding motif, which are present in many proteins whose function is regulated by calcium.

EF-hand Calcium-binding Motif

• The calcium atom is bound to one of the motifs in the muscle protein troponin-C through six oxygen atoms: one each from the side chains of Asp (D) 9, Asn (N) 11, and Asp (D) 13; one from the main chain of residue 15; and two from the side chain of Glu (E) 20. In addition, a water molecule (W) is bound to the calcium atom.

Amino Acid Sequences of EF-hand Motifs

1 3 5 7 9 12

• The side chains of hydrophobic residues on the flanking helices form a hydrophobic core between the helices

• From the sequences above, it can be seen that some residues or types of residues are highly conserved between motifs.

Beta Sheet Topology Diagrams

• Beta sheets are usually represented simply by arrows in topology diagrams that show both the direction of each strand and the way the strands are connected to each other along the polypeptide chain.

transcarbamoylase flavodoxin plastocyanin

The The Hairpin Motif Hairpin Motif

• The hairpin motif is very frequent in sheets and is built up from two adjacent strands that are joined by a loop region.

• For 2 sequentially adjacent hairpin motifs, they can be arranged in 24 different arrangements (conformations)

Bovine Trypsin Inhibitor Snake Venom Erabutoxin

Greek Key Motif

The Greek key motif is found in antiparallel sheets when four adjacent strands are arranged in the pattern shown as a topology diagram in (a). The three dimensional structure of the enzyme Staphylococcus Nuclease shown in (b) in blue and red is also a Greek key motif.

Forming Greek Key Motif

• Suggested folding pathway from a hairpin-like structure to the Greek key motif.

• Beta strands 2 and 3 fold over such that strand 2 is aligned adjacent and antiparallel to strand 1.

Motif

• Two adjacent parallel strands are usually connected by an helix from the C-terminus of strand 1 to the N-terminus of strand 2.

• Most protein structures that contain parallel sheets are built up from combinations of such motifs.

Handedness

• The motif can in principle have two "hands."• (a) This connection with the helix above the sheet is

found in almost all proteins and is called right-handed because it has the same hand as a right-handed helix.

• (b) The left-handed connection with the helix below the sheet.

Adjacent Motifs

Motifs that are adjacent in the amino acid sequence are also usually adjacent in the three-dimensional structure.

Triose-phosphate isomerase is built up from four motifs that are consecutive both in the amino acid sequence (a) and in the three dimensional structure (b).

Domains• "Within a single subunit [polypeptide chain], contiguous

portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981

• Domains may be considered to be connected units, which are to varying extents independent in terms of their structure, function and folding behavior.

• Each domain can be described by its fold. While some proteins consist of a single domain, others consist of several or many. A number of globular protein chains consist of two or three domains appearing as 'lobes'.

• In other cases, the domains may be of a very different nature. For example, some proteins located in cell membranes have a globular intracellular or extracellular domain distinct from that which spans the membrane.

Domain Organization

• Small protein molecules like the epidermal growth factor, EGF, are comprised of only one domain. Others, like the serine proteinase chymotrypsin, are arranged in two domains that are required to form a functional unit. Many of the proteins that are involved in blood coagulation and fibrinolysis have long polypeptide chains that comprise different combinations of domains.

Mosaic Proteins• Mosaic proteins are those which consist of many repeated

copies of one or a few domains, all within one polypeptide chain.

• Many extracellular proteins are of this nature. The domains in question are termed modules and are sometimes relatively small. Note that this term is often applied to sequences whose structures may not be known for certain.

Myosin