Research Collection Doctoral Thesis Interplay between computer simulations and experimental data in physical chemistry and structural biology Testing, interpretation and prediction Author(s): Trzesniak, Daniel Rodrigo Ferreira Publication Date: 2006 Permanent Link: https://doi.org/10.3929/ethz-a-005282239 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETHNO. 16661 Interplay between computer simulations and experimental data in physical chemistry and structural biology: TESTING, INTERPRETATION AND PREDICTION A dissertation submitted to the SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZÜRICH for the degree of Doctor of Sciences presented by Daniel R. F. Trzesniak MSc, University of Sao Paulo (BR) born February 22, 1978 citizen of Brazil accepted on the recommendation of Prof. Dr. Wilfred F. van Gunsteren, examiner Prof. Dr. Beat H. Meier and Dr. Nico F. A. van der Vegt, co-examiners. 2006 Table of contents Table of contents i Acknowledgments v Preface ix About the introduction ix About the rest x Summary xiii Zusammenfassung xv Sommaire xvii SumArio xix Publications xxi Chapter one 1 Introduction Experiment, simulation, computer, biomolecules 1 Classical molecular dynamics simulation 3 9 Free energy, energy and entropy differences Solvation of small molecules 11 Structure of biomolecules 13 References 18 Chapter two 23 A comparison ofmethods to compute a potential ofmean force Summary 23 Introduction 24 Theory 24 Methods 30 Results and discussion 39 Conclusions 42 Acknowledgments 42 References 43 l Table, of con ients Chapter three 49 Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water Summary 49 Introduction 50 Methods 54 Results and discussion 57 Conclusions 62 Acknowledgments 63 References 64 Chapter four 67 M Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 aqueous urea solution Summary 67 Introduction 68 Methods 70 Results and discussion 75 Conclusions 82 Acknowledgments 83 References 84 Chapter five 87 Analysis of neo-pentane-urea pair potentials of mean force in aqueous urea Summary 87 Introduction 88 Theory 89 Methods 91 Results and discussion 93 Conclusions 98 Acknowledgments 99 References 100 ü Table oe contents Chapter six 103 Interpreting NMR data for ß-peptides using molecular dynamics simulations Summary 103 Introduction 104 Methods 107 Results and discussion 109 Conclusions 122 Acknowledgments 124 References 125 Appendix A: NMR data 128 Chapter seven 135 side chains: Simulation of an all-ß3-icosapeptide containing the twenty proteinogenic effect of temperature, pH, counter-ions, solvent andforce field on helix stability 135 S ummary Introduction 136 Methods 137 Results and discussion 139 Conclusions 147 Acknowledgments 148 References 149 Appendix A: NMR data 151 Chapter eight 159 A protein under pressure: molecular dynamics simulation of the Arc Repressor Summary 159 Introduction 160 Methods 162 Results and discussion 165 Conclusions 174 Acknowledgments 175 References 176 iii Table of contents Chapter nine 179 Catalytic mechanism of Cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray cryslallographic and NMR solution data Summary 179 Introduction 180 Methods 181 Results and discussion 183 Conclusions 192 Acknowledgments 192 References 193 Appendix A: Force field parameters for non-standard building blocks 195 Chapter ten 199 Outlook Curriculum vitae 201 iv Acknowledgments make it This part should be a long story. And, knowing myself, I might unintelligible if I do not start from the beginning. Well, not the very beginning though, this 1 leave to the end. I still remember the day 1 went to the Guarulhos airport to fetch Wilfred and for me Jolande. The first is my boss and the latter his wife and the person responsible 1 first being here. OK, this was a joke (not mine though, which is a little suspicious). thank Jolande for being such a lovely person all the time and for helping me to in the future. Wilfred improve my acting skills, which I might use professionally about science here. gave me one of the best periods of my life, and I am not talking Of course there is all the knowledge 1 have tried to catch about molecular dynamics, law, sailing and all the other things I forgot. But what I am talking about is confidence. I thank him for trusting me. For giving me a chance and believing that I could contribute. For this I am eternally grateful. 1 thank Beat Meier for kindly having agreed to be part of this thesis committee. This also applies to Nico. And besides that, I thank him for showing me how amazing entropy can be. his Phil. We never had a project together. My fault, maybe I was too scared by reputation in correcting manuscripts. Funny enough, it was towards the end that we Thereza and had some more time together for a very good conversation. Roberto, family. Thanks to them for all the bottles of wine, the very spicy dishes, the "fur", for all the etc... 1 thank Cris for stealing my house when wc arrived in Zurich and super-funny disagreements we have, which I love! Dr. Bernard Christiaan Oostenbrink. I had overlap in the group with a person who now works at the Vrije Universiteit Amsterdam] Now guess who helped whom? Thanks a lot to Chris for all the support. I thank Prisca for being very easy with the holiday slips. I am also thankful to Daniela, who even being much tougher regarding I want to holidays, helped me with infinitely many things, including my first CV! thank all my dear 1GC 111 students for doing my work, especially Pitschna. v Thanks to Ulf for all those things he did not say. Thanks to Christine for avoiding me to crash IGC that day. Thanks to Tomas for not asking me questions during my talks. Thanks to Peter for teaching me Italian, French, German, Latin, Portuguese and that other language he speaks so nicely. Thanks to Alice for showing diet. me around when I came. Thanks to Tim for not snoring and looking after my this is Thanks to Lovorka for so many times making fun of me in front of people, always great. One danke to Dirk for all the QM projects we have not even started. me how And of course, thanks a lot to Grazia, who once in a while reminded me break important a good dinner can be. I am also grateful to Clara for making my to have a big toe, even if this is not completely true! Vincent, he is the right person laugh with (and what a laugh). And speaking about smiles and related things, thanks cheer. to Jozi. Indi has a beautiful voice and always motivated me with words of Thanks to Bettina (with two "t"s, as she always says) and Maria for taking over the system administration from Markus and me (ha ha!). And speaking about Markus, there arc so many things to mention: the system administration we shared (shared?), the useful discussions (my questions he answered), writing programs together (he but Bea. debugging my code)... and much more. Actually, I should not thank him, Thanks for taking good care of him. And maybe now I am able to convince her to go for diving holidays together, the three of us! Well, look at Merijn for instance. If he had not been there at the Gordon Conference with me, I would not have had the great time I had. And Annemarie joined Mcrijn and I for a wonderful week of fear and loathingl It was really great, thanks to both! And I think Bojan is my source of "cool" phrases to say (verbinde mich). Michel is the perfect buddy for him. Good team, like Starsky & Hutch, Tango & Cash, etc... Thanks! And I know Fang is making a lot of effort to find me a job. I will never forget the Serate da Vino Riccardo and I had. I mean, the first half- hours... And since I mentioned alcohol, thanks to Mika, who can prepare a good 1- part gin/3-parts tonic GT. Thanks to Haibo for having inverted Mika's proportion and Haibo's added some sweetness. And thanks to Moritz not only for having doubled gin doses but also for all the other things that mi cyaan M'rite yah. Daan has been following me since the beginning, literally. My eternal office mate that many times created weird rules when we played games just to win in the end. But that is a detail. I thank him for being there all the time. I also thank Astrid, who even knowing vi Daan's habits always joined our games. Thanks also to the people from the quantum Claire. chemistry group, Hans-Peter and Sankha, with a special merci to Zrinka. I think we do not understand each other. I think she thinks the same. Nevertheless, it has always been fun talking to her, although sometimes I have the impression she gets mad at me. It was very nice of her to lend me her laptop when in time. my hard disk crashed. I am grateful to her for making me finish the thesis Ï thank David, Boris and Alain for allowing me to win a couple of sets. Thanks to Luca for all the mafia tricks he taught me. I will always remember the Brazilian crew here in Zurich: Ricardo and Luciana (especially for driving me to the hospital that day), André and Marina (next time I will let André drive), Marcelo and Lisa (Babaghanoush or Salum? I know what Musa would suggest...), Bruno and Daniel (my gurus) Léo and Mariana (did I get some points??), Eduardo, Ligia and Ignacio (if I write here what wc really do, Ligia kills me!!!).