ATP and its N-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis

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ATP and its N-substituted analogues: parameterization, molecular dynamics simulation and conformational

analysis

Pawel Gruszczyński, Krzysztof Smalara, Michal Obuchowski, Rajmund Kaźmierkiewicz

To cite this version:

Pawel Gruszczyński, Krzysztof Smalara, Michal Obuchowski, Rajmund Kaźmierkiewicz. ATP and its N-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis. Journal of Molecular Modeling, Springer Verlag (Germany), 2010, pp.1081-1090. �10.1007/s00894- 010-0808-3�. �hal-00612404�

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Editorial Manager(tm) for Journal of Molecular Modeling Manuscript Draft

Manuscript Number: JMMO1351R2

Title: ATP and its N6-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis.

Article Type: Original paper

Keywords: Adenosine triphosphate; Molecular Dynamics; Conformational analysis; Simulated Annealing

Corresponding Author: Mr. Paweł Gruszczyński, M.Sc.

Corresponding Author's Institution: University of Gdańsk First Author: Paweł Gruszczyński, M.Sc.

Order of Authors: Paweł Gruszczyński, M.Sc.; Krzysztof Smalara, M.Sc.; Michał Obuchowski, D.Sc.;

Rajmund Kaźmierkiewicz, D.Sc.

Abstract: In this work we used combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of the 12 adenosine triphosphate analogues in water environment. We present simulations in AMBER force field for adenosine triphosphate and its 12 analogues, designed by Shah et al. (Proc Natl Acad Sci U S A, 1997. 94(8): p.

3565-70). The calculations were carried out using GB solvation model with the presence of the magnesium cation Mg2+. The ion was placed in the close distance equal 2Å, from the charged oxygen atoms of beta and gamma phosphate groups of the -3 negatively charged ATP analogue molecules. The analysis of results revealed the distribution of interproton distances H8-H1' and H8-H2' versus the torsional angle ψ (C4-N9-C1'-O4') for all conformations of ATP analogues. There are two gaps in the distribution of torsional angle ψ values, the first is between -30 and 30 degrees described by cis- conformation, and the second is between 90 and 175 degrees which mostly covers region of conformation anti. Our results compare favorably with the results obtained in experimental assays carried out by Jiang, L. and X.-A. Mao in (Polyhedron, 2002. 21(4): p. 435-38).

Response to Reviewers: Dear Editor,

Below are the answers to the suggestions from the decision letter.

Reviewer #1: The sampling methods and the solvent models strongly affect the structures and the dynamics. These are very important issues.

1) If authors perform REMD[1], they would need only a few number of CPU-s (less than ten) and only very short MD phase, because their system is very small. If authors perform Multicanonical simulations [2], they need only one CPU. Because their systems are very small, the 1,000 simulated annealing simulations would be also OK. They should use other enhanced sampling methods (REMD, Multicanonical and so on) in the future.

We are going to follow the Reviewer #1 advice and we will use the more adequate (than the Simulated Annealing) REMD method in the future studies.

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2) "All water models are approximations." It is true. But, the implicit solvent model can not treat the access of water molecules to the solute, while explicit model can treat it. Such effects often affect to the molecular structures. If possible, authors should mention about the validity by short sentence in their paper.

We added the short fragment of text to the current revision of the manuscript. It is located at the end of section "Minimization and SA simulations":

"We are aware that the continuous solvent model is the crude approximation and does not take into account molecular structure of water. It also neglects a lot of modes of interactions like hydrogen bond formation between solute atoms and water, but our results suggest that it is enough to reproduce experimental data. The GB solvent model enabled us quick SA simulations without causing the artifacts in the water structure."

3) In line 18 p.3, authors mentioned that they used simulated annealing and "umbrella sampling methods". They should explain clearly about the umbrella sampling simulations in this paper.

[1] Sugita and Okamoto, CPL 314, 141 (1999) [2] Berg and Neuhaus, Phys Lett B267, 249 (1991)

We just wanted to signal the similarity of our approach to the umbrella sampling method. We were not going to elaborate any further therefore we used words "umbrella sampling methods" only once. To avoid any confusion we removed the reference to the "umbrella sampling methods" in the current revision of the manuscript.

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1.5 2 2.5 3 3.5 4 4.5 5

-180 -150 -120 -90 -60 -30 0 30 60 90 120 150 180

In te rp ro to n d is ta n c e [ a n g s tr .]

Dihedral angle [degree]

Syn conformation

Anti conformation Anti conformation

Cis

-Gauche -Gauche Trans

Trans

Abstract graphic

Click here to download Abstract graphic: graphic_abstract.eps

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1 ATP and its N

⁶

-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis

Received: 07.04.2010 / Accepted: 10.07.2010

Paweł Gruszczyński

^1,2,^

, Krzysztof Smalara

¹

, Michał Obuchowski

³

, and Rajmund Kaźmierkiewicz

²

1

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18/19, 80-952, Gdańsk, Poland

2

Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822, Gdańsk, Poland

3

Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, Dębinki 1, 80-811, Gdańsk, Poland



Email: [email protected]; Tel: +48-58-5235-422; Fax: +48-58-5235-472

Abstract

In this work we used combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of the 12 adenosine triphosphate analogues in water environment. We present simulations in AMBER force field for adenosine triphosphate and its 12 analogues, designed by Shah et al. (Proc Natl Acad Sci USA, 1997. 94(8): p. 3565-70). The calculations were carried out using GB solvation model with the presence of the magnesium cation Mg

²⁺

. The ion was placed in the close distance equal 2Å, from the charged oxygen atoms of beta and gamma phosphate groups of the -3 negatively charged ATP analogue molecules. The analysis of results revealed the distribution of inter-proton distances H8-H1' and H8-H2' versus the torsion angle  (C4-N9-C1'-O4') for all conformations of ATP analogues. There are two gaps in the distribution of torsion angle  values, the first is between -30 and 30 degrees described by cis-conformation, and the second is between 90 and 175 degrees which mostly covers region of conformation anti. Our results compare favorably with the results obtained in experimental assays carried out by Jiang, L.

and X.-A. Mao in (Polyhedron, 2002. 21(4): p. 435-38).

manuscript

Click here to download Manuscript: JMM1351R2_final.doc

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2 Keywords Adenosine triphosphate  Molecular Dynamics  Conformational analysis  Simulated Annealing

Abbreviations

ATP Adenosine triphosphate

MD Molecular Dynamics

SA Simulated Annealing

A*TP Adenosine triphosphate derivatives RESP Restrained electrostatic potential

GB Generalized Born

VDW Van der Waals

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3 Introduction

Adenosine triphosphate (ATP) is one of the most important molecules, present in all of the cells of living organisms. This high-energetic nucleotide powers most biochemical processes which require energy by several different ways. One of them is transferring a phosphate group to another molecule in a process called phosphorylation. This reaction is carried out by enzymes called kinases. Identification of substrates that are phosphorylated by specific kinases is difficult because of the enormous number of these enzymes and also, kinases display overlapping substrate specificities [1-2].The approach presented by Shah et al. [3] is based on using mutatated kinases, that enlarge ATP-binding pocket and ATP analogues, whose specificity allows to find substrates of kinase. This method has been used successfully for Rous sarcoma virus tyrosine kinase [3].

The process of designing complementary ATP-analogues with modified kinases has to be started with understanding of conformational behavior of the nucleotide and assurance that modification introduced to ATP does not change the conformational properties of this molecule. We study in this work the conformation of ATP molecule and its 12 analogues proposed by Shah et al. [3] bound with magnesium cation (Mg

²⁺

) using molecular dynamics (MD) simulation enhanced with simulated annealing (SA). We present a full set of AMBER force-field parameters for each of the ATP analogue, which provides possibility to use models of molecules in other computational experiments, such as docking and molecular modeling of interaction between the analogues and kinases.

After discovery of protein kinase activity in 1954 [4] the field of protein kinase drug

discovery has dramatically advanced. More and more researchers are involved in designing of

new kinase inhibitors, as the pharmaceutical industry is focused on this subject. Molecular

modeling is one of the most helpful tools in that area. For example, it was successfully used in

studies on inhibitors of: vascular endothelial growth factor receptor tyrosine kinase [5],

cyclin-dependent kinase family [6-7], as well as in case of serine-threonine kinases: p38 [8],

Aurora A [9] or checkpoint kinase 1 [10]. Models presented in this work, together with their

AMBER force-field parameters, can also be used for modeling kinase inhibitors as well as for

designing different than shown here ATP-analogues.

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4 Methods

Initial models

The ATP analogues which are considered in this work were taken from a set presented by Shah et al. [3]. Models of the molecules of ATP analogues were built using MOLDEN [11]

and additionally a model of the ATP molecule from Structural Cambridge Database (entry ADENTP03 [12]) was used as a template. Two of the ATP analogues models, namely N

⁶

- methoxy ATP (AT

¹

P) and N

⁶

-pyrrolidino ATP (AT

⁷

P) were built in our previous work [13].

Hybridizations of atom N

⁶

in ATP-derivatives were determined by comparison with molecules having the N-substituent group attached to aromatic ring. The comparison of crystal structures to the ATP-models is shown in the Table 1.The charge of the ATP and its analogues was -3, consistently with models presented by Shah et al. [3]. Parameterization of the ATP analogues to the AMBER force field proceeded as recommended in the AMBER [14] manual. Restrained electrostatic potential (RESP) was used to obtain partial atomic charges of ATP and its twelve analogues. Structures of the models were subjected to geometry optimization at the level HF/6-31G* using an ab-initio chemistry package GAMESS [15]. Charges were calculated from optimized geometries using R.E.D. (see http://q4md-forcefieldtools.org/RED/). Complete set of information about assigned atom types and atomic charges we included in LEaP Object File Format (OFF) files deposited in the form of electronic supplementary material. All modifications introduced to AMBER force field [16], which were used to parameterize ATP analogues, are included in Table 2.

ATP requires the presence of divalent cation, usually magnesium, which is coordinated by ATP phosphate groups. The presence of ion is crucial for obtaining proper conformation by ATP but also very important in catalyzing phosphotranspher reaction [17], particularly in kinases [18]. To each model of ATP molecule one magnesium cation Mg

²⁺

was added using LEaP command addIons. The addIons procedure places the counterion in a shell around one or more ATP analogue anion using a Coulombic potential on a grid.

The reason why only one magnesium cation was added can be found in our previous work

[13, 19], where ATP and two ATP-derivatives respectively were docked to the serine-

threonine kinase, PrkC and only one magnesium ion was found near the phosphates. An

extensive studies by Martinez et al. [20] on ATP conformations and ion bindings modes in the

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5 active site of anthrax edema factor also supported mechanism of kinase activity based on the presence of one magnesium cation in the active site of the enzyme.

The magnesium cation was held using distance restraints during the SA simulations. To obtain an input distance restraints we have calculated distances between magnesium ion and four oxygen atoms of the phosphate groups beta and gamma (see Fig. 1), from initial structures after using addIons command. The values of distances varied between 2.0 and 4.5 Å. These values were used as boundary values and the force constants for distance restraints were 20 kcal mol

^{-1 .}

Å on each of the four distances (Mg--O1B, Mg--O2B, Mg--O1G and Mg- -O2G).

Minimization and SA simulations

Initial structures of ATP and its analogues were optimized with SANDER, part of the AMBER 9.0 package [14] using Steepest Descent minimization for 5000 steps and followed by the 15000 steps of conjugate gradient minimization. Subsequently, all models were submitted to 50 ps (50000 steps with 1 fs time step) run of Simulated Annealing (SA) protocol for a 1000 times. Single SA protocol consisted of four stages (see Fig. 2):

1) 0-2 ps Short equilibration

2) 2-10 ps Heating from 300K to 1200K 3) 10-40 ps Slow cooling from 1200K to 300K 4) 40-50 ps Equilibration at 300K

Each set of final coordinates from one SA simulation was used as a starting point for the following simulation. It is worth to note, that there is a short equilibration period, at the first stage of SA run, before heating stage. Running the heating procedure, immediately after minimization, brings the instabilities to the system and causes unusually high energy.

The simulations were carried out using the implicit solvent model, namely the Generalized

Born (GB) solvation model developed by Onufriev, Bashford and Case (GB

^OBC

) [21]. We are

aware that the continuous solvent model is the crude approximation and does not take into

account molecular structure of water. It also neglects a lot of modes of interactions like

hydrogen bond formation between solute atoms and water, but our results suggest that it is

enough to reproduce experimental results. The GB solvent model enabled us quick SA

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6 simulations without causing the artifacts in the water structure. For temperature regulation we used the Langevin thermostat [22] and a collision rate of 1 ps

^-1

.

Analysis

Analysis of the  angle vs. the inter-proton distance H8-H1' and H8-H2'

The calculations of the torsion angle , defined as O4’-C1’-N9-C4, and inter-proton distances (H8-H1' and H8-H2') were calculated using PTRAJ, module of AMBER 9 [14] based on the final structures from each of the simulation. Collected data are presented in Fig. 3 which was created using the gnuplot program (http://www.gnuplot.info). Points illustrating the dependence between the torsion angle (O4’-C1’-N9-C4) and inter-proton distances were fitted to the function: f   x = A * sin   x  o  / B)  + C (Fig. 3, panel A). Parameters obtained after the fitting procedure are presented in Table 1S (see Supplementary materials). Fitting was done only for calculations concerning the ATP, to visualize the shape of the plot of this function.

Results and discussion

Here we report the results of the conformational analysis carried out after the Molecular Dynamics simulations.

Magnesium cation restraints

The distances between magnesium and oxygen atoms (O) were measured to verify if the magnesium cation was kept by the restraints during our simulations. An illustration of what is happening during a single Simulated Annealing (SA) run is presented in Fig. 1. We show only the first run for the ATP, because the rest of the runs, for ATP and its derivatives, are similar and do not show any significant variations.

Fig. 1 shows that the distances between Mg

²⁺

cation and four of the charged oxygen atoms

²⁺

cation almost at the same distances. Close distance also represents stronger ion interaction between magnesium cation and the negatively charged oxygen atoms. Occurrences of the distance values in the range between 2 Å and 3.5 Å are very rare because this position is energetically unfavorable.

Analysis of the distribution of the values of torsion angle O4’-C1’-N9-C4

ATP conformation can be partially defined by value of the torsion angle between atoms: O4’-

C1’-N9-C4 (see Fig. 1S). If the value varies between 0±90 degrees, then the conformation is

denoted as “syn” and if the value varies between 180±90 degrees than the conformation is

denoted as “anti”. We checked the distribution of values in conformations of our models,

which were submitted to Simulated Annealing MD. Values of the dihedral angle (O4’-C1’-

N9-C4) were measured for each of the snapshot taken after the equilibration stage. In the

Table 3, we present measured values of the torsion angle for each of the ATP-analogues. As

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8 an example of distribution of the analyzed dihedral angle we also present a Fig. 5, which shows a distribution of values of O4’-C1’-N9-C4 angle in the ATP.

Both, Table 3 and Fig. 5, clearly show that there are two maxima in the frequency of occurrence of the torsion angle value. The first maximum is present around -120 degrees (conformation anti) and the second maximum is around 60 degrees (conformation syn). The ATP molecule or its analogue frequently adopts the conformation anti when it binds inside the ATP-binding pocket. The results show that the first maximum is broad and the other is rather sharp. These two maxima represent two major sets of conformations of ATP and their analogues, and the transitions between them may be essential for the activation of the kinases.

The dependence between O4’-C1’-N9-C4 angle and inter-proton distances H8-H1’/H8- H2’

The distribution of conformations of ATP can also be partially described using analysis of the inter-proton distances H8-H1' and H8-H2' versus the torsion angle  (C4-N9-C1'-O4'). This analysis was previously applied by Jiang and Mao [24] for the interpretation of combined NMR and molecular modeling experiments on unmodified ATP molecules. Comparison of our results and those obtained by Jiang and Mao, shows that we observe the same structural behavior. From Fig. 3 we can clearly conclude that there are two main conformations of ATP model, the first, which is mostly the conformation anti with the  angle value of -120±60 degrees and the second (syn) with the  angle value of 45±30 degrees. The two least frequent conformations are characterized by  angle values of -30±30 and 120±30 respectively.

Dihedral angle C4-N9-C1’-O4’ analysis shows that in the case of ATP as well as in the case

of presented ATP-analogues there are two gaps in the distribution of angle values ranges, the

first is between -30 and 30 degrees described by cis-conformation, and the second is between

90 and 175 degrees which mostly covers region of conformation anti, which are presented on

the right side of the Fig. 3, panel A. The cis-conformation is forbidden only for some of the

ATP analogue models, namely 3, 7, 10 and 12 (see Fig. 3, panel B). This is transitional

conformation between, the “inactive conformation” ( angle values around 60) and “active

conformation” ( angle values range around 160). By the “active conformation” we mean

such a conformation of the ATP which is able to form complex with protein. If the molecule

conformation falls into inactive state and the cis-conformation is forbidden, than there is no

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9 possibility to change the conformation into active-state. This conformational “gap” can possibly decrease the binding affinity of such a ligand. This thesis explains the results of biological experiments, namely low values of inhibition for ATP-analogues 3, 7 and 10 studied by Shokat and coworkers [3, 25].

The second region is forbidden for all of the ligands, ATP and its derivatives. To understand why the second region is forbidden for all of the ATP models we calculated the energetic profile for the ATP model changing the torsion angle by rotating the adenine ring. We observed the increase of Van der Waals (VDW) energy in the second forbidden- conformational state (data not shown). Close distances between adenine nitrogen atom N9 and hydrogen H2’ and H3’ atoms from ribose ring were revealed by visual inspection of the conformation.

To summarize, the anti-conformation is not allowed due to sterical effects in all of the models but, on the contrary, the presence of cis-conformation is crucial for biological activity.

How ATP conformation does depend on conformation of sugar?

The conformational change between active and inactive stage is only possible trough the cis- conformation. The role of the ribose conformation might also be significant in obtaining the active/inactive stage. To verify this hypothesis we calculated the relationship of  angle and torsion angle between atoms C1’-C2’-C3’-C4’, which defines the sugar conformation (see Fig. 1S and Fig. 6). The most commonly populated sugar conformations [26] were: the C3’- endo region, corresponding to a torsion angle around 35°, and C2’-endo region with the torsion angle values around -35°.

We observed that rotation of the adenine depends on the conformation of the sugar. In the Fig.

6 we present four main conformations, two in the active state and two in inactive state. One of

the conformations in the inactive state is preferable and reflects C2’-endo sugar conformation

and the torsion  angle around 45 degrees. For most of the analogues it is not possible to

change the adenine position from the inactive to active state having the C2’-endo

conformation. Furthermore the switch between active and inactive state is possible with the

C3’-endo sugar conformation, present. The same conformational behavior was observed in

case of the ATP molecule. Focusing on the active conformation, we observed, that it is also

favorable when sugar is in the C2’-endo conformation.

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10 We speculate that the changes of the sugar conformation are involved in the transition from the inactive into active states of the ATP analogues, and the sequence of changes includes the following stages:

5) C2’-endo cis-conformation inactive 1) C3’-endo cis-conformation

2) C3’-endo anti-conformation

3) C2’-endo anti-conformation active It is also presented in the Fig. 6, panel A.

Summary

In this work we present parameters introduced to AMBER force field and Molecular Dynamics calculations for adenosine triphosphate and its 12 analogues, proposed by Shah et al. [3] with one magnesium cation Mg

²⁺

. The ion was found in the close, distance equal 2Å, from the charged oxygen atoms of beta and gamma phosphate groups of the ATP analogue molecule. Analyzing the O4’-C1’-N9-C4 dihedral angle values, which partially describe the conformation of adenosine triphosphate (and its N

⁶

-substituted derivatives), we discovered the existence of two maxima. One, sharp maximum located near +60° value of the angle and called by us an “inactive-state” and second, broad maximum located close to -120°, called an

“active-state”. The active-state conformation is frequently found when ATP is bound into the ATP-binding pocket in the kinases. Change between the states is possible only trough cis- conformation (0±30°) which is not allowed for all of the ATP-analogues, namely AT

³

P, AT

⁷

P, AT

¹⁰

P and AT

¹²

P. These results corresponds to the findings made by Shah et al. [3], explaining low values of inhibition activity of those ATP-derivatives with wild-type and mutant of the Rous sarcoma tyrosine kinase. Additionally, we found the character of the contribution of the conformation of the ribose ring into the transition between the inactive- /active-state. The path from the inactive-state to active-state leads through changes between C2’-endo and C3’-endo of the sugar.

Substitutions proposed by Shah et al. on the N

⁶

, adenine atom of the ATP, do not influence

the main conformational properties of the nucleoside. Parameters introduced by us to

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11 AMBER force field tested by MD simulations gave reasonable results on the conformational matter which are comparable to the experimental values [Polyhedron, 21, 435-438 (2002)].

Acknowledgments

We would like to acknowledge Dr. Artur Sikorski for accessing the Cambridge Structural

Database and for his valuable help during the research.

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15 Tables

Table 1 Hybridization of the N

⁶

⁷

P – hybidization is sp2, and not sp3 as was accidentially witten in our previous work

[Gruszczynski QSAR 2007]

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16 Table 2 Parameters introduced to the AMBER force field

Bond Parameters

CA-N N2-OS H –OH

481. 1.340 448. 1.365 553. 0.960

Angle Parameters

H -OH-P CA-N2-OS N2-OS-CT H -N2-OS OS-CT-HC OS-CT-CA N2-CT-HC N2-CT-CA CT-N2-CT CB-CA-N CA-N -H CA-N -C NC-CA-N

45.0 108.500 70.0 120.000 60.0 117.000 50.0 121.200 50.0 109.500 50.0 109.500 50.0 109.500 80.0 111.200 50.0 109.500 70.0 123.500 50.0 120.000 50.0 121.900 70.0 119.300

Dihedral Parameters

CA-N2-OS-CT H -N2-OS-CT CB-CA-N -H CB-CA-N -C NC-CA-N -H NC-CA-N -C

4 7.50 180.0 2.

4 7.50 0.0 2.

4 9.60 180.0 2.

Improper Parameters

HC-CT-OS-HC 1.1 180. 2.

(21)

17 Table 3 Occurrences of dihedral O4’-C1’-N9-C4 angle value within small, 30° degrees ranges

AT

^x

P/

P

-180 0 0 0 0 0 0 0 0 0 0 0 0 0

-150 71 36 46 108 98 61 155 78 80 152 90 34 151

-120 246 72 66 223 149 136 134 212 178 186 222 115 216

-90 194 106 132 189 123 175 109 129 137 123 157 148 133

-60 96 143 199 100 114 106 96 34 72 47 69 190 57

-30 12 70 77 19 27 40 39 7 18 22 20 74 13

0 7 35 20 8 10 7 34 4 6 36 4 19 5

30 74 55 51 15 72 68 83 60 28 108 17 31 29

60 225 316 263 199 309 334 261 352 360 260 334 273 288

90 63 154 128 136 75 69 75 121 114 56 81 112 98

120 2 11 6 0 1 0 4 3 0 1 0 2 1

150 0 0 1 0 0 0 0 0 0 0 0 0 0

180 10 2 11 3 22 4 10 0 7 9 6 2 9

(22)

18 Figure captions

Fig. 1 Distance restraints held the magnesium cation (Mg

²⁺

) close to the charged oxygen atoms (atom types O1B, O1G, O2B and O2G) of the phosphates (2.0-4.5 Å)

Fig. 2 Time/temperature dependence during single simulated annealing MD run.

Simulated Annealing protocol is shown in the box

Fig. 3 Dihedral O4’-C1’-N9-C4 angle dependence on inter-proton distances H8-H1' (presented as crosses) and H8-H2' (shown as dots) measured for ATP (panel A) and its analogues (panel B). This plot can be compared to the plot presented by Jiang et al.[24] which results were obtained from CNS experiment

Fig. 4 The distance between the magnesium cation (Mg

²⁺

) and oxygen atoms from beta and gamma phosphate groups (O1B, O1G, O2B and O2G) in each of the MD run, calculated for the ATP

Fig. 5 Distribution of values of the dihedral angle O4’-C1’-N9-C4, partially defining the conformation of ATP obtained in 1000 MD runs. There are two maxima, first present around -120 degrees (conformation anti) and the second around 60 degrees (conformation syn)

Fig. 6 Dihedral O4’-C1’-N9-C4 angle dependence on sugar conformation, described by dihedral C1’-C2’-C3’-C4’angle measured for ATP (panel A) and its analogues (panel B). In the panel A, we also present schematic conformational transition from inactive to active state. The conformations were not clustered but we only indicated (black boxes in panel A) those, that were close to each other

Figure caption supplementary figure

Fig. 1S Structure of the ATP molecule with the C4-N9-C1’-O4’ torsion angle indicated by

the blue lines and with the C1’-C2’-C3’-C4’ torsion angle indicated by the red lines

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MD simulation time [ps]

1 2 3 4 5

O1B---MG

1 2 3 4

O1G---MG

1 2 3 4

Di stan ce betw een m agn es iu m a n d o xyge n a toms [ Å ]

O2B---MG

1 2 3 4

0 5 10 15 20 25 30 35 40 9 50

O2G---MG

OO 1 G OO 2 G OO 1 B OO 2 B NH2

Mg2+

P

O O

P O OH

P

O OO

O O

O N N

N N

OH OH

Figure 1

Click here to download line figure: Figure1.eps

(24)

200 300 400 500 600 700 800 900 1000 1100 1200 1300

0 5 10 15 20 25 30 35 40 45 50

Te m p e ra tu re [ K ]

MD simulation time [ps]

0 – 2ps Equlibrate at 300K

2 – 10ps Heating from 300K to 1200K 10 – 40ps Slow cooling form 1200K to 300K 40 – 50ps Equlibrate at 300K

Figure 2

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1.5 2 2.5 3 3.5 4 4.5 5

-180 -150 -120 -90 -60 -30 0 30 60 90 120 150 180

Interproton distance [angstr.]

Dihedral angle [degree]

Syn conformation

Anti conformation Anti conformation

Cis

-Gauche -Gauche Trans

Trans

1 2 3 4 5

-180 0 180

1.

1 2 3 4 5

-180 0 180

2.

1 2 3 4 5

-180 0 180

3.

1 2 3 4 5

-180 0 180

4.

1 2 3 4 5

-180 0 180

5.

1 2 3 4 5

-180 0 180

6.

1 2 3 4 5

-180 0 180

7.

1 2 3 4 5

-180 0 180

8.

1 2 3 4 5

-180 0 180

9.

1 2 3 4 5

-180 0 180

10.

1 2 3 4 5

-180 0 180

11.

1 2 3 4 5

-180 0 180

12.

B

A

Figure 3

(26)

1.5 2 2.5 3 3.5 4 4.5 5

0 100 200 300 400 500 600 700 800 900 1000

Mg--O1B Mg--O1G Mg--O2B Mg--O2G

Molecular Dynamics run

Di stan ce [ Å]

Figure 4

(27)

0 50 100 150 200 250

-150 -120 -90 -60 -30 0 30 60 90 120 150 180

Dihedral χ angle [°]

F requ en c y

Figure 5

(28)

-45 -30 -15 0 15 30 45

-180 0 180

1.

-45 -30 -15 0 15 30 45

-180 0 180

2.

-45 -30 -15 0 15 30 45

-180 0 180

3.

-45 -30 -15 0 15 30 45

-180 0 180

4.

-45 -30 -15 0 15 30 45

-180 0 180

5.

-45 -30 -15 0 15 30 45

-180 0 180

6.

-45 -30 -15 0 15 30 45

-180 0 180

7.

-45 -30 -15 0 15 30 45

-180 0 180

8.

-45 -30 -15 0 15 30 45

-180 0 180

9.

-45 -30 -15 0 15 30 45

-180 0 180

10.

-45 -30 -15 0 15 30 45

-180 0 180

11.

-45 -30 -15 0 15 30 45

-180 0 180

12.

A

B

Dihedral C4-N9-C1’-O4’ angle [degree]

Dihedral C1'’-C2’-C3’-C4’ angle [degree]

-60 -45 -30 -15 0 15 30 45 60

-180 0 180

inactive active

Figure 6

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Table 1S. Function and parameters which were used to fit points of the dependence between dihedral angle , defined as O4’-C1’-N9-C4 and inter-proton distances H8-H1' and H8-H2'. Panel A includes the results from ATP and panel B includes the results for twelve ATP derivatives.

H8-H1' vs χ H8-H2' vs χ

function f(x) = Asin((x-o)/B)+C f(x) = Asin((x-o)/B)+C parameters A = -0.711497 +/- 0.004059 (0.5705%)

o = 62.8525 +/- 1.163 (1.85%) B = 57.3327 +/- 0.4238 (0.7392%) C = 3.25103 +/- 0.003892 (0.1197%)

A = 1.22124 +/- 0.0248 (2.031%) o = 29.1328 +/- 1.154 (3.962%) B = 55.266 +/- 0.6866 (1.242%) C = 3.52014 +/- 0.02212 (0.6284%) convergence WSSR : 10.2536

delta(WSSR) : -3.51109e-06

delta(WSSR)/WSSR : -3.42424e-07 limit for stopping : 1e-05

lambda : 6.24729e-08 ndf: 996

sqrt(WSSR/ndf): 0.101463 WSSR/ndf: 0.0102948

WSSR : 78.0605 delta(WSSR) : -7.68945e-06

delta(WSSR)/WSSR : -9.85062e-08 limit for stopping : 1e-05

lambda : 5.77892e-06 ndf: 996

sqrt(WSSR/ndf): 0.279954 WSSR/ndf: 0.078374

WSSR - final sum of squares of residuals delta(WSSR)/WSSR - rel. change during last iteration

ndf - degrees of freedom

sqrt(WSSR/ndf) - rms of residuals

WSSR/ndf - variance of residuals (reduced chisquare)

Supplementary material - Table 1S

Click here to download attachment to manuscript: Table1s.doc

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CH ₂

NH ₂

O − O −

P O

O

OH HO

N N

N

O O

O P

P

O O

HO

C4−N9−C1’−O4’

Supplementary material - Figure1S

Click here to download attachment to manuscript: Figure1S.eps

(31)

!!index array str "zw0"

!entry.zw0.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg "O3G" "OH" 0 1 131072 1 8 -0.720600

"H" "H" 0 1 131072 2 1 0.393900 "PG" "P" 0 1 131072 3 15 1.161100 "O2G" "O2" 0 1 131072 4 8 -0.818800 "O1G" "O2" 0 1 131072 5 8 -0.818800 "O3B" "OS" 0 1 131072 6 8 -0.396500 "PB" "P" 0 1 131072 7 15 0.889400 "O1B" "O2" 0 1 131072 8 8 -0.720050 "O2B" "O2" 0 1 131072 9 8 -0.720050 "O3A" "OS" 0 1 131072 10 8 -0.327500 "PA" "P" 0 1 131072 11 15 0.918700 "O1A" "O2" 0 1 131072 12 8 -0.725450 "O2A" "O2" 0 1 131072 13 8 -0.725450 "O5*" "OS" 0 1 131072 14 8 -0.409500 "C5*" "CT" 0 1 131072 15 6 0.021400 "H50" "H1" 0 1 131072 16 1 0.093500 "H51" "H1" 0 1 131072 17 1 0.093500 "C4*" "CT" 0 1 131072 18 6 0.298400 "H40" "H1" 0 1 131072 19 1 0.104900 "O4*" "OS" 0 1 131072 20 8 -0.481600 "C1*" "CT" 0 1 131072 21 6 0.038600 "H10" "H1" 0 1 131072 22 1 0.183500 "N9" "N*" 0 1 131072 23 7 -0.066600 "C8" "CK" 0 1 131072 24 6 0.187200 "H80" "H5" 0 1 131072 25 1 0.190100 "N7" "NB" 0 1 131072 26 7 -0.609800 "C5" "CB" 0 1 131072 27 6 0.087800 "C6" "CA" 0 1 131073 28 6 0.634600 "N6" "N2" 0 1 131073 29 7 -0.836000 "H61" "H" 0 1 131073 30 1 0.374700 "H62" "H" 0 1 131073 31 1 0.374700 "N1" "NC" 0 1 131073 32 7 -0.804700 "C2" "CQ" 0 1 131073 33 6 0.619000 "H2" "H5" 0 1 131073 34 1 0.021100 "N3" "NC" 0 1 131073 35 7 -0.732000 "C4" "CB" 0 1 131072 36 6 0.338600 "C3*" "CT" 0 1 131072 37 6 0.107300 "H30" "H1" 0 1 131072 38 1 0.062400 "O3*" "OH" 0 1 131072 39 8 -0.651800 "H32" "HO" 0 1 131072 40 1 0.377800 "C2*" "CT" 0 1 131072 41 6 0.151800 "H20" "H1" 0 1 131072 42 1 0.090800 "O2*" "OH" 0 1 131072 43 8 -0.689400 "H33" "HO" 0 1 131072 44 1 0.439900

!entry.zw0.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg "O3G" "OH" 0 -1 0.0

"H" "H" 0 -1 0.0 "PG" "P" 0 -1 0.0 "O2G" "O2" 0 -1 0.0 Supplementary material

Click here to download attachment to manuscript: atp.off.txt

(32)

"O1G" "O2" 0 -1 0.0 "O3B" "OS" 0 -1 0.0 "PB" "P" 0 -1 0.0 "O1B" "O2" 0 -1 0.0 "O2B" "O2" 0 -1 0.0 "O3A" "OS" 0 -1 0.0 "PA" "P" 0 -1 0.0 "O1A" "O2" 0 -1 0.0 "O2A" "O2" 0 -1 0.0 "O5*" "OS" 0 -1 0.0 "C5*" "CT" 0 -1 0.0 "H50" "H1" 0 -1 0.0 "H51" "H1" 0 -1 0.0 "C4*" "CT" 0 -1 0.0 "H40" "H1" 0 -1 0.0 "O4*" "OS" 0 -1 0.0 "C1*" "CT" 0 -1 0.0 "H10" "H1" 0 -1 0.0 "N9" "N*" 0 -1 0.0 "C8" "CK" 0 -1 0.0 "H80" "H5" 0 -1 0.0 "N7" "NB" 0 -1 0.0 "C5" "CB" 0 -1 0.0 "C6" "CA" 0 -1 0.0 "N6" "N2" 0 -1 0.0 "H61" "H" 0 -1 0.0 "H62" "H" 0 -1 0.0 "N1" "NC" 0 -1 0.0 "C2" "CQ" 0 -1 0.0 "H2" "H5" 0 -1 0.0 "N3" "NC" 0 -1 0.0 "C4" "CB" 0 -1 0.0 "C3*" "CT" 0 -1 0.0 "H30" "H1" 0 -1 0.0 "O3*" "OH" 0 -1 0.0 "H32" "HO" 0 -1 0.0 "C2*" "CT" 0 -1 0.0 "H20" "H1" 0 -1 0.0 "O2*" "OH" 0 -1 0.0 "H33" "HO" 0 -1 0.0

!entry.zw0.unit.boundbox array dbl -1.000000

0.0 0.0 0.0 0.0

!entry.zw0.unit.childsequence single int 2 !entry.zw0.unit.connect array int 0 0

!entry.zw0.unit.connectivity table int atom1x int atom2x int flags

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1 2 1 1 3 1 3 4 1 3 5 1 3 6 1 6 7 1 7 8 1 7 9 1 7 10 1 10 11 1 11 12 1 11 13 1 11 14 1 14 15 1 15 16 1 15 17 1 15 18 1 18 19 1 18 20 1 18 37 1 20 21 1 21 22 1 21 23 1 21 41 1 23 24 1 23 36 1 24 25 1 24 26 1 26 27 1 27 28 1 27 36 1 28 29 1 28 32 1 29 30 1 29 31 1 32 33 1 33 34 1 33 35 1 35 36 1 37 38 1 37 39 1 37 41 1 39 40 1 41 42 1 41 43 1 43 44 1

!entry.zw0.unit.hierarchy table str abovetype int abovex str belowtype int belowx "U" 0 "R" 1

"R" 1 "A" 1 "R" 1 "A" 2 "R" 1 "A" 3 "R" 1 "A" 4

(34)

"R" 1 "A" 5 "R" 1 "A" 6 "R" 1 "A" 7 "R" 1 "A" 8 "R" 1 "A" 9 "R" 1 "A" 10 "R" 1 "A" 11 "R" 1 "A" 12 "R" 1 "A" 13 "R" 1 "A" 14 "R" 1 "A" 15 "R" 1 "A" 16 "R" 1 "A" 17 "R" 1 "A" 18 "R" 1 "A" 19 "R" 1 "A" 20 "R" 1 "A" 21 "R" 1 "A" 22 "R" 1 "A" 23 "R" 1 "A" 24 "R" 1 "A" 25 "R" 1 "A" 26 "R" 1 "A" 27 "R" 1 "A" 28 "R" 1 "A" 29 "R" 1 "A" 30 "R" 1 "A" 31 "R" 1 "A" 32 "R" 1 "A" 33 "R" 1 "A" 34 "R" 1 "A" 35 "R" 1 "A" 36 "R" 1 "A" 37 "R" 1 "A" 38 "R" 1 "A" 39 "R" 1 "A" 40 "R" 1 "A" 41 "R" 1 "A" 42 "R" 1 "A" 43 "R" 1 "A" 44

!entry.zw0.unit.name single str "BBB"

!entry.zw0.unit.positions table dbl x dbl y dbl z 6.875640 2.351660 0.056618

6.630302 3.106590 0.596087 5.420386 2.076180 -0.500847 5.450223 2.333732 -1.939434 4.534879 2.886501 0.368979 5.108550 0.545302 -0.187770 3.612050 0.125750 0.164808 2.718846 0.578782 -0.899090 3.321019 0.780205 1.469795

(35)

3.634613 -1.457254 0.343091 2.280187 -2.290172 0.454652 1.630795 -2.348282 -0.868369 2.620614 -3.593037 1.077050 1.273249 -1.520871 1.453533 0.199004 -0.715312 0.961796 -0.174851 -0.074833 1.757440 0.576620 -0.082374 0.156034 -0.972381 -1.552232 0.432126 -0.709511 -2.608422 0.445544 -2.114918 -1.361190 1.254545 -3.273534 -1.295954 0.431238 -4.007953 -2.043913 0.734844 -3.881068 0.050750 0.553144 -3.378120 1.169983 1.172540 -2.411258 1.181264 1.659466 -4.159894 2.214898 1.107543 -5.292415 1.723121 0.438522 -6.544532 2.251466 0.057487 -6.986054 3.464005 0.310241 -6.484906 4.090331 0.924316 -7.931821 3.646109 0.023675 -7.407962 1.525838 -0.645448 -7.080697 0.283862 -0.964802 -7.806836 -0.265456 -1.550664 -5.971664 -0.368367 -0.639500 -5.120372 0.414664 0.073514 -1.366616 -1.161532 -0.997617 -1.310125 -0.077618 -1.080955 -0.589974 -1.797218 -2.026409 0.324184 -1.972315 -1.650530 -2.834988 -1.578946 -1.009721 -3.410356 -1.012441 -1.742938 -2.919038 -2.960058 -1.273328 -2.246730 -3.110770 -1.953178

!entry.zw0.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x 0 0 0 0 0 0

!entry.zw0.unit.residues table str name int seq int childseq int startatomx str restype int imagingx "BBB" 1 45 1 "?" 0

!entry.zw0.unit.residuesPdbSequenceNumber array int 0

!entry.zw0.unit.solventcap array dbl -1.000000

0.0 0.0 0.0 0.0

!entry.zw0.unit.velocities table dbl x dbl y dbl z 0.0 0.0 0.0

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

(36)

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

(37)

!!index array str "zw1"

!entry.zw1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg "N9" "N*" 0 1 131074 1 7 -0.083200

"C4" "CB" 0 1 131074 2 6 0.465200 "C5" "CB" 0 1 131074 3 6 0.002200 "N7" "NB" 0 1 131074 4 7 -0.615800 "C8" "CK" 0 1 131074 5 6 0.169700 "H80" "H5" 0 1 131074 6 1 0.207400 "C6" "CA" 0 1 131074 7 6 0.503300 "N1" "NC" 0 1 131074 8 7 -0.747200 "C2" "CQ" 0 1 131074 9 6 0.592400 "H2" "H5" 0 1 131074 10 1 0.028000 "N3" "NC" 0 1 131074 11 7 -0.744900 "N6" "N2" 0 1 131074 12 7 -0.244000 "H60" "H" 0 1 131072 13 1 0.304200 "C1*" "CT" 0 1 131074 14 6 0.050400 "H10" "H1" 0 1 131074 15 1 0.167400 "O4*" "OS" 0 1 131074 16 8 -0.442000 "C4*" "CT" 0 1 131074 17 6 0.200900 "H40" "H1" 0 1 131074 18 1 0.122600 "C3*" "CT" 0 1 131074 19 6 0.094100 "H30" "H1" 0 1 131074 20 1 0.054100 "C2*" "CT" 0 1 131074 21 6 0.280700 "H20" "H1" 0 1 131074 22 1 0.019800 "C5*" "CT" 0 1 131074 23 6 0.007700 "H50" "H1" 0 1 131074 24 1 0.100000 "H51" "H1" 0 1 131074 25 1 0.100000 "O5*" "OS" 0 1 131074 26 8 -0.444500 "P3" "P" 0 1 131074 27 15 1.072700 "O3A" "OS" 0 1 131074 28 8 -0.402700 "P2" "P" 0 1 131074 29 15 0.949600 "O3B" "OS" 0 1 131074 30 8 -0.390000 "P1" "P" 0 1 131074 31 15 1.141500 "O2G" "O2" 0 1 131072 32 8 -0.816650 "O3*" "OH" 0 1 131074 33 8 -0.645000 "H32" "HO" 0 1 131074 34 1 0.407600 "O2*" "OH" 0 1 131074 35 8 -0.713900 "H33" "HO" 0 1 131074 36 1 0.436300 "O3G" "OH" 0 1 131072 37 8 -0.719100 "H" "H" 0 1 131074 38 1 0.395300 "O1G" "O2" 0 1 131073 39 8 -0.816650 "O2B" "O2" 0 1 131072 40 8 -0.728400 "O1B" "O2" 0 1 131072 41 8 -0.728400 "O1A" "O2" 0 1 131072 42 8 -0.771500 "O2A" "O2" 0 1 131072 43 8 -0.771500 "O5" "OS" 0 1 131074 44 8 -0.234700 "C62" "CT" 0 1 131074 45 6 0.000200 "H26" "HC" 0 1 131074 46 1 0.062200 "H36" "HC" 0 1 131074 47 1 0.062200 "H16" "HC" 0 1 131074 48 1 0.062200

!entry.zw1.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg Supplementary material

Click here to download attachment to manuscript: zw1.off.txt

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"N9" "N*" 0 -1 0.0 "C4" "CB" 0 -1 0.0 "C5" "CB" 0 -1 0.0 "N7" "NB" 0 -1 0.0 "C8" "CK" 0 -1 0.0 "H80" "H5" 0 -1 0.0 "C6" "CA" 0 -1 0.0 "N1" "NC" 0 -1 0.0 "C2" "CQ" 0 -1 0.0 "H2" "H5" 0 -1 0.0 "N3" "NC" 0 -1 0.0 "N6" "N2" 0 -1 0.0 "H60" "H" 0 -1 0.0 "C1*" "CT" 0 -1 0.0 "H10" "H1" 0 -1 0.0 "O4*" "OS" 0 -1 0.0 "C4*" "CT" 0 -1 0.0 "H40" "H1" 0 -1 0.0 "C3*" "CT" 0 -1 0.0 "H30" "H1" 0 -1 0.0 "C2*" "CT" 0 -1 0.0 "H20" "H1" 0 -1 0.0 "C5*" "CT" 0 -1 0.0 "H50" "H1" 0 -1 0.0 "H51" "H1" 0 -1 0.0 "O5*" "OS" 0 -1 0.0 "P3" "P" 0 -1 0.0 "O3A" "OS" 0 -1 0.0 "P2" "P" 0 -1 0.0 "O3B" "OS" 0 -1 0.0 "P1" "P" 0 -1 0.0 "O2G" "O2" 0 -1 0.0 "O3*" "OH" 0 -1 0.0 "H32" "HO" 0 -1 0.0 "O2*" "OH" 0 -1 0.0 "H33" "HO" 0 -1 0.0 "O3G" "OH" 0 -1 0.0 "H" "H" 0 -1 0.0 "O1G" "O2" 0 -1 0.0 "O2B" "O2" 0 -1 0.0 "O1B" "O2" 0 -1 0.0 "O1A" "O2" 0 -1 0.0 "O2A" "O2" 0 -1 0.0 "O5" "OS" 0 -1 0.0 "C62" "CT" 0 -1 0.0 "H26" "HC" 0 -1 0.0 "H36" "HC" 0 -1 0.0 "H16" "HC" 0 -1 0.0

!entry.zw1.unit.boundbox array dbl -1.000000

0.0 0.0

(39)

0.0 0.0

!entry.zw1.unit.childsequence single int 2

!entry.zw1.unit.connect array int 0 0

!entry.zw1.unit.connectivity table int atom1x int atom2x int flags 1 2 1

1 5 1 1 14 1 2 3 1 2 11 1 3 4 1 3 7 1 4 5 1 5 6 1 7 8 1 7 12 1 8 9 1 9 10 1 9 11 1 12 13 1 12 44 1 14 15 1 14 16 1 14 21 1 16 17 1 17 18 1 17 19 1 17 23 1 19 20 1 19 21 1 19 33 1 21 22 1 21 35 1 23 24 1 23 25 1 23 26 1 26 27 1 27 28 1 27 42 1 27 43 1 28 29 1 29 30 1 29 40 1 29 41 1 30 31 1 31 32 1 31 37 1 31 39 1 33 34 1

(40)

35 36 1 37 38 1 44 45 1 45 46 1 45 47 1 45 48 1

!entry.zw1.unit.hierarchy table str abovetype int abovex str belowtype int belowx "U" 0 "R" 1

"R" 1 "A" 1 "R" 1 "A" 2 "R" 1 "A" 3 "R" 1 "A" 4 "R" 1 "A" 5 "R" 1 "A" 6 "R" 1 "A" 7 "R" 1 "A" 8 "R" 1 "A" 9 "R" 1 "A" 10 "R" 1 "A" 11 "R" 1 "A" 12 "R" 1 "A" 13 "R" 1 "A" 14 "R" 1 "A" 15 "R" 1 "A" 16 "R" 1 "A" 17 "R" 1 "A" 18 "R" 1 "A" 19 "R" 1 "A" 20 "R" 1 "A" 21 "R" 1 "A" 22 "R" 1 "A" 23 "R" 1 "A" 24 "R" 1 "A" 25 "R" 1 "A" 26 "R" 1 "A" 27 "R" 1 "A" 28 "R" 1 "A" 29 "R" 1 "A" 30 "R" 1 "A" 31 "R" 1 "A" 32 "R" 1 "A" 33 "R" 1 "A" 34 "R" 1 "A" 35 "R" 1 "A" 36 "R" 1 "A" 37 "R" 1 "A" 38 "R" 1 "A" 39 "R" 1 "A" 40 "R" 1 "A" 41 "R" 1 "A" 42 "R" 1 "A" 43 "R" 1 "A" 44

(41)

"R" 1 "A" 45 "R" 1 "A" 46 "R" 1 "A" 47 "R" 1 "A" 48

!entry.zw1.unit.name single str "2"

!entry.zw1.unit.positions table dbl x dbl y dbl z -3.317169 -0.458713 0.204572

-4.683152 -0.396266 -0.001214 -5.047450 0.899261 0.262774 -3.920313 1.679417 0.597012 -2.945195 0.803616 0.600358 -1.921789 1.043648 0.856159 -6.439010 1.126680 0.140887 -7.266564 0.142257 -0.177177 -6.758581 -1.051893 -0.436734 -7.458564 -1.827986 -0.730362 -5.486708 -1.420448 -0.382557 -7.065534 2.281941 0.277840 -6.589170 3.126947 0.565872 -2.460857 -1.656901 0.046821 -3.068217 -2.543534 0.218832 -1.402375 -1.603822 0.994463 -0.163179 -1.713764 0.307281 0.181081 -2.738061 0.375757 -0.386575 -1.367954 -1.169136 -0.289409 -0.290173 -1.304403 -1.848171 -1.763719 -1.353230 -2.346623 -1.114886 -2.071737 0.853995 -0.769191 0.948237 1.287024 -0.141660 0.171838 0.330378 -0.139188 1.661961 1.899273 -1.476370 1.611591 3.081453 -2.211458 0.797955 4.266436 -1.145042 0.692081 4.031902 0.339433 0.125359 5.490913 0.965577 -0.041472 5.647864 2.486942 -0.487639 4.538981 3.308826 0.063118 0.490774 -2.067523 -2.066640 1.380758 -2.183662 -1.632043 -1.884025 -3.098706 -1.796699 -1.092821 -3.172619 -2.359969 6.900373 2.946124 0.350487 6.419948 3.670669 0.742666 6.016855 2.595501 -1.902405 3.345313 0.312025 -1.160989 3.365817 1.185616 1.154350 2.565563 -2.538807 -0.540660 3.533852 -3.358204 1.611015 -8.458805 2.256755 0.141781 -8.968006 3.548580 0.313544

(42)

-10.051738 3.528873 0.207418 -8.706540 3.913550 1.305633 -8.542345 4.209475 -0.440214

!entry.zw1.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x 0 0 0 0 0 0

!entry.zw1.unit.residues table str name int seq int childseq int startatomx str restype int imagingx "2" 1 49 1 "?" 0

!entry.zw1.unit.residuesPdbSequenceNumber array int 0 !entry.zw1.unit.solventcap array dbl

-1.000000 0.0 0.0 0.0 0.0

!entry.zw1.unit.velocities table dbl x dbl y dbl z 0.0 0.0 0.0

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

(43)

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0