alexey potapov. phd thesis in published papers format

8/14/2019 Alexey Potapov. PhD Thesis in published papers format

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Thesis for the degreeDoctor of Philosophy

ByAlexey Potapov

Advisor:Daniella Goldfarb

September 2009

Submitted to the Scientific Council of theWeizmann Institute of Science

Rehovot, Israel

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Development of pulsed EPR methods at high field and their application to studiesof metalloproteins and model systems.

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Acknowledgment s .

I would like to express my sincere gratitude and respect to my advisor Daniella Goldfarb.

Her energetic enthusiasm, strongest motivation, patience and profound knowledge had animmense impact on this work. I am also grateful to our collaborator and a good friend

Arnold Raitsimring for sharing with us his EPR wisdom..

This thesis would never be possible without Boris Epel, whose support of Specman

software throughout all these years helped us to broaden enormously the scope of pulsed

EPR experiments at high-field. I am heartily thankful to Yakov Lipkin and Yehoshua

Gorodecki who have assembled a novel W-band EPR bridge which became a real proud of

the EPR group at WIS. The freeze-quench work was inspired in part by my trip to the lab

of Friedhelm Lendzian- a brilliant scientist and a hospitable host. I would like to thank also

our collaborators: Irit Sagi, Gottfried Otting, Thomas Meade, David Mistein, Harry Gray

and their students and posdocs whose skillful hands have prepared almost every sample in

this work: Barak Akabayov, Gunanathan Chidambaram, Ying Song, Hiromasa and Kyle

Lancaster. I acknowledge and appreciate valuable comments and encouragement provided

by my thesis committee - Shimon Vega, Jacob Anglister and Lucio Frydman.

I am very much indebted to Ilia Kaminker for reviving the DbpA project at the moment

when clouds of skepticism have shadowed our bright expectations. I really appreciate our

many fruitful and inspiring discussions about EPR and science in general. This work would

not be complete without generous help of Akiva Feintuch, who invested his time into

careful editing of this text. Also I am grateful to my other labmates: Marina, Michal, Marc,

Erez and Vijaj for creating and keeping a warm and friendly atmosphere at work.

My final, and most heartfelt, acknowledgment must go to my wife Larisa. Her support in

all my undertakings scientific and otherwise, her encouragement and immense patience has

turned my PhD studies into a pleasure. For all that and for everything else she brings in my

life she has my everlasting love.

http://en.wikipedia.org/wiki/Acknowledgment

http://en.wikipedia.org/wiki/Acknowledgment



Abstract.In this work we developed a pulsed EPR (pEPR) methodology relevant to studies of bi-

ological systems and applied high-…eld (95 GHz) pEPR tools to investigate active sites in

metalloproteins.

In the …rst part, dedicated to development of methods, we initially tackled the problem

of congested nuclear spectra obtained using ELDOR (electron–electron double resonance)-

detected NMR and ENDOR (electron-nuclear double resonance) measurements. We intro-

duced a new triple resonance hyper…ne sublevel correlation spectroscopy (THYCOS) sequence

based on the combination of ENDOR and ELDOR-detected NMR experiments in a way sim-

ilar to the TRIPLE experiment. It allows correlating nuclear frequencies belonging to the

same electron spin manifold. The method provides links between forbidden electron transi-

tions ( M S = 1; M I 6= 0) and allowed nuclear transitions,( M S = 0 ; M I = 1) ; thus

facilitating the assignment of nuclear frequencies to their respective paramagnetic sites and

electron manifolds. It also yields the relative signs of the hyper…ne couplings of the nuclei. The

feasibility of the method was demonstrated …rst on a single crystal of Cu2+ -doped L-histidine

and on a frozen solution of Cu2+ –histidine complexes. Then we applied THYCOS to resolve

ENDOR spectra of ascorbate oxidase, an enzyme containing two Cu2+ binding sites, type 1(T1) and type 2 (T2), with overlapping EPR spectra. In both sites the Cu2+ is coordinated

to histidine residues, the hyper…ne coupling of which can be determined by several pulse EPR

high resolution techniques, but the assignment of the14 N signals to their respective Cu2+ site is

ambiguous. We show that using THYCOS, the14 N signals of T1 can be unambigously identi…ed

through correlations with the1 H signals of the cysteine -protons of T1.

Another issue addressed in the methodological part concerns the problem of distance mea-surements at high-…elds. There, the typically used nitroxide spin labels have several shortcom-

ings and another approach is needed. We examined the possibility of using Gd3+ (S=7/2) as

potential spin label for distance measurements. As a …rst step towards this goal we carried

out pulse double electron-electron resonance (DEER) W- and Ka -band distance measurements

between two high spin Gd3+ ions in a novel bis-Gd3+ complex involving two pyridine based

gadolinium tetracarboxylate systems linked by a rigid aryl-alkyne unit. The experimental dis-tance found was 2.020.02 nm and it was further compared with the Gd3+ -Gd3+ distance



(2.2126 nm) determined by density functional theory. Then we have shown that DEER is able

to probe broad distance distributions in dimers with Gd3+ ions connected via a ‡exible linker.

This demonstrated the feasibility of distance measurements in systems with large and low de-

gree of disorder, and the potential for using Gd3+ based labels as a substitute for nitroxide at

high-…eld.

Additionally, we set the basis for studies of intermediates in enzymatic reactions using

rapid freeze-quench high-…eld EPR. We designed a simple set-up for rapid-freeze quench EPR

at W-band. It is based on a BioLogic commercial apparatus and a modi…ed sample collection

appropriate for W-band capillaries. The standard reaction of myoglobin with azide, which

converts high spin Fe(III) to low spin Fe(III), used for calibration of rapid freeze quench X-

band EPR, is very inconvenient for high …eld measurements. Here we proposed a di¤erent

simple calibration reaction for W-band; the reduction of a nitroxide free radical with sodium

dithionite using Mn2+ as an internal standard. Using this calibration reaction we determined

the dead-time of our system to be less than 10 ms.

In the second part we concentrated on applications of high-…eld pEPR methods for studies

of metals in proteins. First, we addressed the coordination of Mn2+ ion in the active site of

the RNA helicase DbpA. As a start we characterized the coordination shell of Mn2+ in somesimple inorganic complexes serving as models for binding site in the protein. W-band (95 GHz)

pulsed ENDOR measurements were carried out to probe quantitatively the …rst coordination

shell of Mn2+ bound to ADP and ATP S. The intensity of the ENDOR e¤ect was used for

counting the number of equivalent phosphate oxygens and water ligands. The comparison of

the 31 P ENDOR e¤ect of the 1:1 ADP and ATP S complexes shows that two phosphates are

coordinated in both; while in ADP they are equivalent, in ATP S they are slightly di¤erent.The coordination of bicarbonate to Mn2+ was explored as the simplest model system for

the coordination of Mn2+ by carboxylate residues of the protein. Here we showed that both

Davies and Mims ENDOR should be recorded for a reliable assignment and that the blind spots

should be accounted to obtain unique set of hyper…ne parameters. These showed that either

a couple of distinct sites with slightly inequivalent13 C nuclei (Aiso 1 =1.2 MHz T? 1 =0.7 MHz

Aiso 2 =1.0 T? 2 =0.6 MHz) is present or that there is distribution of geometries. The sign of the

hyper…ne was determined by variable mixing time (VMT) ENDOR measurements. The dis-



tances extracted from T? 1 ;T? 2 (3.05-3.2 Å) are consistent with a complex of two monodentate

bicarbonates bound to Mn2+ ion. This conclusion was further supported by DFT calculations.

Next we apply the same ENDOR methods for studies of DbpA ATPase active site. It is

known that DbpA undergoes a conformational change upon binding of RNA and ATP S. We

intended to elucidate the origin of these changes by probing the close environment of Mn2+ ,

substituting the essential Mg2+ ion. We have found the displacement of some water molecules

and phosphates away from the coordination shell of Mn2+ -nucleotide upon its binding to the

protein. 13 C-ENDOR of Mn2+ ADP bound to 13 C-labeled DbpA revealed the presence of a

nucleus at the de…ned Mn2+ -13 C distance of 3.8 Å in complex of Mn2+ ADP DbpA, while no

de…ned distance was found in complex of Mn2+ ATP S DbpA. The line shape in the spectra did

not change upon binding of RNA. These results indicate that the the conformational change

upon RNA binding does not a¤ect the close vicinity of Mn2+ ion. A reduction of 13 C-ENDOR-

e¤ect accompanied by the observation of 31 P-ENDOR signals characteristic for Mn2+ RNA , was

detected for the complex Mn2+ ADP DbpA, but not for Mn2+ ATP S DbpA, showing higher

a¢nity fo ATP S to Mn2+ .

Finally, we applied high-…eld pEPR for characterizing the electronic structure of Cu2+ in the

C121D azurin mutant, where an additional mutation of axial ligand (Met) is introduced. Themutation of axial methionine by a hydrophobic amino acid yields a copper binding site with

unusual EPR spectrum not belonging to type 1 or type 2 copper sites. It was initially suggested

that the mutation of axial methionine in C112D azurin causes redistribution of the electron

and spin density in the equatorial plane. We observe only a slight decrease in the nitrogen

hyper…ne couplings upon substitution of the axial methionine by a hydrophobic amino acid.

Therefore, we conclude that the decrease of spin density on the metal ion is not associated withan increased spin density on the equatorial histidine ligands.



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Аннотация .

В данной работе мы развиваем методологию импульсного электронного парамагнитного

резонанса (ЭПР ), в приложении к изучению биологических систем , и используем

инструменты высокопольного импульсного ЭПР для исследования активных центров в

металлопротеинах .

В первой части работы , посвященной развитию методов , мы решаем проблему сложных

ядерных спектров , полученных с помощью методик ЭЛДОР -(электрон -электронный

двойной резонанс ) -детектированного ЯМР (ЭД - ЯМР ) и ДЭЯР (двойной электрон -

ядерный резонанс ). Мы предлагаем новую трёхрезонансную корреляционную

спектроскопию сверхтонких подуровней (THYCOS), последовательность которой есть

комбинация экспериментов ЭД - ЯМР и ДЭЯР . Методика позволяет соотнести ядерные частоты принадлежащие одному мультиплету уровней с одной заданной проекцией

электронного спина . Метод позволяет связать запрещённые электронные переходы

(∆M S =±1, M I 6=0) и разрешённые ядерные переходы (∆M I 6=±1), тем самым способствуя

отнесению ядерных частот к их соответствующим парамагнитным центрам и

электронным мультиплетам . Также метод даёт относительные знаки сверхтонкого

взаимодействия электрона и ядер . Реализуемость метода была показана сперва на

монокристалле L-гистидина допированного ионами Cu2+. Затем мы применили THYCOS

для того чтобы разрешить ДЭЯР спектры аскорбат оксидазы - энзима содержащего два

Cu 2+ активных центра ( тип 1 и тип 2 ) с перекрывающимися спектрами ЭПР . В обоих

центрах Cu 2+ координирован гистидиновыми аминокислотными остатками , чьи

сверхтонкие константы могут быть определены с помощью нескольких ЭПР методик

высокого разрешения , тем не менее , отнесение 14 N сигналов к соответствующему Cu 2+

центру не является однозначным . Мы демонстрируем , что , используя THYCOS, 14 N

сигналы могут быть однозначно отнесены к типу 1 с помощью их корреляций с

наблюдаемыми сигналами протонов цистеина в центре Т1.

Вторая проблема , затронутая в методической части , касается вопроса измерения

расстояний в высоких полях . Обычно используемый нитроксильный радикал имеет ряд

недостатков , и потому требуется другой подход . Мы изучили возможность

использования Gd 3+ (S=7/2) в качестве потенциальной спиновой метки для измерения

расстояний . На первой стадии мы провели импульсные высокопольные (W- band , Ka-

band) измерения расстояний методом двойного электрон -электронного резонанса



(ДЭЭР ) между двумя высокоспиновыми ионами Gd 3+ в новом бис -Gd 3+ комплексе ,

включающем две Gd 3+-тетракарбоксилатных системы на основе пиридина , связанные

жестким арил -алкиленовым мостиком . Экспериментально измеренное расстояние около

2.02±0.02 нм сравнимо с расчётным (2.2126 нм), которое получено с помощью теории

функционала плотности . Затем мы показали , что ДЭЭР подходит для исследования

распределения расстояний в димерах с ионами Gd 3+, соединенными гибким мостиком .

Это продемострировало выполнимость измерений расстояний в системах с большой и

малой степенью неупорядоченности , а также потенциал использования меток на основе

Gd 3+ в высоком поле в качестве замены нитроксильным радикалам .

Также мы закладываем основание для исследований промежуточных продуктов

энзиматических реакций с помощью высокопольного ЭПР , используя метод гашения

реакции быстрой заморозкой . Мы разработали простую установку для быстрой

заморозки образцов для W-band спектрометра . Она основана на коммерческом аппарате

BioLogic и модифицированной системе для сбора образцов в измерительную кювету .

Стандартная реакция миоглобина с азидом , которая переводит Fe(III) из состояния с

большим спином в состояние с малым спином , используемая для калибровки быстрой

заморозки на образцах для X-band спектрометра , неудобна для измерений в высоком

поле . Мы предлагаем другую калибровочную реакцию : восстановление свободного

нитроксильного радикала натрий дитионитом , используя ионы Mn 2+ в качестве

внутреннего стандарта интесивности линий . Используя предложенную калибровочную

реакцию , мы определили «мёртвое время » нашей системы как меньшее 10 мс.

Во второй части мы сосредоточились на приложениях методов импульсного ЭПР для

изучения активных белковых центров , содержащих металлы . Во-первых , мы

рассмотрели координацию иона Mn 2+ в активном центра РНК -геликазы DbpA. Для

начала мы охарактеризовали координинационную оболочку Mn 2+ в некоторых

неорганических комплексах , служащих моделями для центра связывания в белке .

Импульсные ДЭЯР (W-band) измерения были выполнены для того , чтобы дать

количественное описание ближайшей координационной оболочке Mn 2+, связанного с

АДФ и АТФ γS. Интенсивность линий ДЭЯР (ДЭЯР -эффект ) была использована для

оценки числа эквивалентных фосфатов и молекул воды . Сравнение 31P ДЭЯР -эффектов

у 1:1 АДФ и АТФ γS показала , что в обоих комплексах координированы два фосфата : у

АДФ они эквивалентны (в смысле спектров ), тогда как у АТФ γS — слегка различаются .



Координация бикарбоната к Mn 2+ была изучена на простейшей модельной системе ,

имитирующей связывание Mn 2+ аминокислотными остатками белка . Мы показали , что

для надежного отнесения линий необходимо записываить и Davies, и Mims ДЭЯР , а

также , что «слепые » участки в спектрах должны быть учтены для того , чтобы получить

единственный набор сверхтонких постоянных . Наше исследование показало наличие

либо пары слегка различающихся в смысле спектров 13С ядер , либо разброс геометрий

комплекса . Знак сверхтонкой постоянной был определён с помощью ДЭЯР измерений с

изменяемым временем смешивания (VMT-ENDOR). Полученные расстояния находятся

в согласии с моделью комплекса , состоящего из двух молекул бикарбоната

монодентатно связанных с Mn 2+. В дальнейшем этот вывод также был подтверждён

вычислениями методом функционала плотности .

Далее мы применяем те же самые методы ДЭЯР для изучения активного центра

гидролиза АДФ у DbpA. Известно , что DbpA испытывает изменение конформации при

связывании РНК и АДФ γS . Мы намеревались прояснить природу этих изменений ,

исследуя ближайшее окружение иона Mn 2+, замещающего необходимый для катализа

Mg 2+. Мы обнаружили вымещение нескольких молекул воды и фосфатов из

координационной оболочки Mn 2+ в комплексе с нуклеотидом при его связывании с

белком . 13С - ДЭЯР комплекса Mn 2+-AДФ , связанного с 13С-меченным DbpA, обнаружил

присутствие ядра на определённом расстоянии в 3.8 А для комплекса Mn 2+-АДФ -DbpA,

в то же время не было обнаружено ядра с определённым расстоянием в комплексе Mn 2+-

АТФ γS-DbpA- РНК . Форма линии не меняется при связывании с РНК . Эти результаты

указывают на то, что конформационное изменение при связывании РНК не затрагивает

ближайшее окружение иона Mn 2+. Уменьшение ДЭЯР -эффекта , сопровождаемое

наблюдением сигналов 31P-ДЭЯР , характерных для Mn 2+-РНК , было обнаружено для

комплекса Mn 2+-АДФ -DbpA, но не для комплекса Mn 2+-АТФ γS-DbpA, тем самым

показавая более высокое сродство Mn 2+ к АТФ γS.

Наконец , мы применили высокопольный импульсный ЭПР для описания электронной

структуры Сu2+ в мутированном белке азурине (С112D), где добавлена дополнительная

мутация аксиального лиганда (метионин ). Замена аксиального лиганда на гидрофобную

аминокислоту даёт центр связывания Cu 2+ с необычным ЭПР спектром не

принадлежащим ни к типу 1, ни к типу 2. Изначально было предложено , что мутация

аксиального метионина в азурине C112D вызывает перераспределение электронной и

спиновой плотности в экваториальной плоскости . Мы обнаружили лишь небольшое



уменьшение сверхтонких констант азота при замене аксиального метионина

гидрофобной аминокислотой . Поэтому мы заключаем , что уменьшение спиновой

плотности на ионе металла не связано с увеличенной спиновой плотностью на

экваториальных лигандах гистидина .



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|βα +>

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ωα

ωβ

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|ββ −>

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ωα

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sin( θ/2 )2 sin( θ/2 )2

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sin( θ/2 )2 sin( θ/2 )2

f f a a

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sin( θ/2 )2 sin( θ/2 )2

f f a a

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sin( θ/2 )2 sin( θ/2 )2

f f a a

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sin( θ/2 )2 sin( θ/2 )2

f f a a

cos( θ/2 )2 cos( θ/2 )2

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MW 2

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MW 2

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MW 2

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MW

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MW 2

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ΗΤ Α

MW

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MW

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>96-2

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250 G

200 G

150 G

100 G

50 G

Hydrophobic:M121LM121FM121I

Others:M121MM121HM121E

250 G

200 G

150 G

100 G

50 G

250 G

200 G

150 G

100 G

50 G

250 G

200 G

150 G

100 G

50 G

Hydrophobic:M121LM121FM121I

Others:M121MM121HM121E

?=KH; 79> FE?DJ E< J>; :?7=H7C C7HAI = 7D: L7BK;I E< 7 K FHEJ;?D 7:7,;< 5 6 ,;: C7HAI I>EM J>; FHEJ;?DI C;7IKH;: ?D MEHA 5 6

JOF; ! JOF; ! * L7BK;I E< 7I I>EMD ?D ?= .>; 7KJ>E

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J>; :;DI?JO ?D J>; ;GK7JEH?7B FB7D; .>7J 97D 8; FHE8;: 8O C;7IKH?D= J>; B?=7D: >O

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FHEJEDI 7D: :?H;9JBO 9EEH:?D7J;: >?IJ?:?D;( KI?D= 1 7D: FKBI;: ( ), 7J 2 87D: 5 6

5 6 7D: H;CEJ; ?C?:7PEB;( KI?D= - ' 7D: FKBI;: ( ), 5 6 5 6 5 6 5 6 .>; :?H;9JBO

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<EH 9ECFB;J; IF;9JHEI9EF?9 9>7H79J;H?P7J?ED I?D9; J>; DK9B;7H 4;;C7D ?DJ;H79J?ED >7

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3%07

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C;7IKH;C;DJI

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IJK:O E< J>; 8?97H8ED7J; 8?D:?D= JE 'D

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KDKIK7B *, FHEF;HJ?;I E8I;HL;: 8O 9EDL;DJ?ED7B C;J>E:I ?D J>; CKJ7DJI M?J> 7N?7B

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)8,3( ():)0341)28

86-40) 6)732%2') ,=4)6?2) 79&0):)0 '366)0%8-32 )<4)6-1)28 *36

%77-+21)28 3* )0)'8632 29'0)%6 (39&0) 6)732%2') 0-2)7

*EJ7FEL F;B 7D: 7D?;BB7 !EB:<7H8 JH?FB; H;IED7D9; >OF;HRD; IK8B;L;B

;NF;H?C;DJ <EH 7II?=DC;DJ E< ;B;9JHED DK9B;7H :EK8B; H;IED7D9; B?D;I $ >;C



!)730:-2+ 0-+%2( ,=4)6?2) '3940-2+7 3* 3:)60%44-2+ 8=4) %2(

9 -2 %7'36&%8) 3<-(%7) &= 8,) ,-+, ?)0( 4907) ! '36

6)0%8-32 74)'863'34=

*EJ7FEL # *;9>J !EB:<7H8 IK8C?JJ;:



#,) 2 &-'%6&32%8) '3140)< -2 % *63>)2 73098-32 6):-7-8)( &=

4907)( $ &%2( !

*EJ7FEL !EB:<7H8 .>; 'D8?97H8ED7J; 9ECFB;N ?D 7 <HEP;D IEBKJ?ED H;L?I?J

FKBI;: 1 87D: ( ), #DEH= >;C



( 3140)<)7 %7 38)28-%0 "4-2 %&)07 *36 -+, -)0( 907)(

! -78%2') )%796)1)287

!: ECFB;N;I 7I *EJ;DJ?7B -F?D &78;BI <EH "?=> ?;B: *KBI;: *, ?IJ7D9; ';7IKH;C;DJI

' ,7?JI?CH?D= !KD7D7J>7D *EJ7FEL #H;D7 <H;C;DAE $7D ' & '7HJ?D'?BIJ;?D 7D: 7D?;BB7 !EB:<7H8 $ C >;C -E9



)}(exp{)( t C t V ir

ir ia t V t V t V )()()(

)()}({ t C / t ir lnV λ

randomly distributed in space, the time pattern, V(t), is the product of two patterns, V(t) ia

and V(t) ir , resulting from intra- (ia) and inter- (ir) pair dipolar interactions :

(9)

For S=1/2 (to a good accuracy)

(10)

where C is the spin concentration (mM) and t is the time interval ( s). The flip

probability, λ, therefore, can be evaluated from the experimental time domain DEER

trace V(t) ir as

(11)

Likewise, n(½)

can be estimated from the experimental time domain DEER traceV (t )ir ,½ stemming from the inter Gd(III) dipolar interaction for known concentrations.

3.5 Determination of the distance distribution from time domain patterns

There are two simple approaches that can be used in combination or separately to

determine the approximate pair distribution function, both of which are based on

processing the DEER time domain pattern . One processes the entire time domain trace of

V (t )ia while the other makes use of the dependence of the asymptotic decaya

iat V )( on

pulse durations. In the following, we briefly describe both methods as they were applied

to pairs composed of S= ½ centers.

If the pulse durations used in DEER are short (1/t p>> dd), then the V (t )ia of pairs which

have an intrapair distance distribution, f(r) , and which are randomly oriented with respect

to the magnetic field is

(12))dr )r ( f )t Acos(()dx)t Acos()r ( f dr ()t (V zz

______________

zz nnia0

1

101111



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2800 2900 3000 3100 3200 3300 3400

magnetic field, mT

C112D/M121L

C112DC112D/M121F

C112D/M121L

C112D

2800 2900 3000 3100 3200 3300 3400

magnetic field, mT

2800 2900 3000 3100 3200 3300 3400

magnetic field, mT

C112D/M121L

C112DC112D/M121F

C112D/M121L

C112D

2800 2900 3000 3100 3200 3300 3400

magnetic field, mT

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-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6ν−ν RF, MHz

-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6

ν−ν RF, MHz

*

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32'097-327

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remote exchangeablehydrogens

Hydrogens with largestcoupling A ||=12 MHz

Similar to wild typeazurin

Options: a)A 1~37 and

A 2~27, or b)A~32 MHz;significant anisotropy

A || ~161 G

Axial [2.063 2.063 2.311]

C112D

Hydrogens with largestcoupling A || =10 MHz

Hydrogens with largest coupling A ||=12 MHz

W-band ENDORHydrogens


Similar to wild type azurinX-band HYSCOREImidazoleremote nitrogens

-----remote exchangeablehydrogens

W-band ENDORExchangablehydrogens

A~20 MHz small

anisotropy

A~20 MHz. small anisotropyW-band ED-NMR,

HYSCORE

Close nitrogens

A ||~108 G A ||~108 GX-band CWHyperfinecoupling of

63,65 Cu a

Rhombic [2.066 2.0872.387]

Rhombic [2.047 2.119 2.385]X-band CWg-values a

C112D/M121FC112D/M121LExperiment

remote exchangeablehydrogens

Hydrogens with largestcoupling A ||=12 MHz


Options: a)A 1~37 and

A 2~27, or b)A~32 MHz;significant anisotropy

A || ~161 G

Axial [2.063 2.063 2.311]

C112D

Hydrogens with largestcoupling A || =10 MHz

Hydrogens with largest coupling A ||=12 MHz

W-band ENDORHydrogens


Similar to wild type azurinX-band HYSCOREImidazoleremote nitrogens

-----remote exchangeablehydrogens

W-band ENDORExchangablehydrogens

A~20 MHz small

anisotropy

A~20 MHz. small anisotropyW-band ED-NMR,

HYSCORE

Close nitrogens

A ||~108 G A ||~108 GX-band CWHyperfinecoupling of

63,65 Cu a

Rhombic [2.066 2.0872.387]

Rhombic [2.047 2.119 2.385]X-band CWg-values a

C112D/M121FC112D/M121LExperiment

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ED J>; 97H8ENOB =HEKF E< J>; 7IF7HJ?9 79?: .>?I MEKB: H;GK?H; IJK:?;I E< 7 B78;BB;: FHEJ;?D

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-1.0 -0.5 0.0 0.5 1.0

-1.000

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-0.985

n o r m a

l i z e d e c h o

i n t e n s i t y

Mn-ADP-DbpAMn-ADP-DbpA-RNAsimulation

νRF-νC13, MHz

?=KH; .>; '?CI ( ), IF;9JH7 E< J>; 'D * 8F 9ECFB;N M?J>EKJ ,( 8B79AM>;H; 5'D *6 C' 5 8F 6 C' M?J> ,( H;: M>;H; J>; I7C; 9ED9;DJH7J?EDI 7D:5,( 6 C' -?CKB7J?ED M?J> . '"P 7 $ '"P 8BK;

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-8 -6 -4 -2 0 2 4 6 8

MnADPDbpA+RNA 100 mM KCl

Mn-RNA 100 mM KCl

νRF-ν31P, MHz

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J>; 9EDJH?8KJ?EDI E< JME 9ECFED;DJI

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-1.0 -0.5 0.0 0.5 1.0

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-0.994

n o r m a

l i z e d e c h o

i n t e n s i t y

νRF-ν13C

MnATP γS-DbpAMnATP γS-DbpA-RNA

?=KH; .>; '?CI ( ), IF;9JH7 E< J>; 'D .* - 8F 9ECFB;N M?J>EKJ ,( 8B79AM>;H; 5'D .* - 6 C' 5 8F 6 5,( 6 C' M?J> ,( H;:

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-1.00

-0.99

-0.98

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-0.96

-0.95

Mn-ADP-DbpAMn-ATP γS-DbpAresidual water signal

e c h o

i n t e n s i t y

νRF , MHz

AII feature of H 2O

b

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alexey potapov. phd thesis in published papers format

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