From experimental, structural probability distributions to the theoretical causality analysis of molecular changes

Daniluk, P.; Dziubiński, M.; Lesyng, B.; Hallay-Suszek, M.; Rakowski, F.; Walewski, Ł.

Artykuł - szczegóły

Tytuł artykułu

From experimental, structural probability distributions to the theoretical causality analysis of molecular changes

Autorzy

Daniluk P. , Dziubiński M. , Lesyng B. , Hallay-Suszek M. , Rakowski F. , Walewski Ł.

Wybrane pełne teksty z tego czasopisma

http://cames.ippt.gov.pl/

Identyfikatory

Warianty tytułu

Języki publikacji

Abstrakty

A brief overview of causality analysis (CA) methods applied to MD simulations data for model biomolecular systems is presented. A CausalMD application for postprocessing of MD data was designed and implemented. MD simulations of two model systems, porphycene (ab initio MD) and HIV-1 protease (coarse-grained MD) were carried out and analyzed. Granger’s causality methodology based on a Multivariate Autoregressive (MVAR) formalism, followed by the Directed Transfer Function (DTF) analysis was applied. A novel approach based on the descriptors of local structure was also presented and prelim- inary results were reported. Casuality analyses are required for a better understanding of biomolecular functioning mechanisms. In particular, such analyses can link physics-based structural dynamics with functions inferred from molecular evolution processes. Current limitations and future developments of the presented methodologies are indicated.

Słowa kluczowe

causality analysis signal analysis local descriptors alignment MVAR Directed Transfer Function molecular dynamics porphycene HIV-1 protease molecular function molecular evolution

analiza przyczyn analiza sygnałów deskryptory lokalne wyrównanie MVAR dynamika molekularna porficyny proteazy HIV-1 funkcja molekularna ewolucja molekularna

Wydawca

Instytut Podstawowych Problemów Techniki PAN

Czasopismo

Computer Assisted Methods in Engineering and Science

Rocznik

2012

Tom

Vol. 19, no. 3

Strony

257--276

Opis fizyczny

Bibliogr. 57 poz., rys., tab., wykr.

Twórcy

autor

Daniluk P.

autor

Dziubiński M.

autor

Lesyng B.

autor

Hallay-Suszek M.

autor

Rakowski F.

autor

Walewski Ł.

Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences Pawińskiego 5, 02-106 Warsaw, Poland, lesyng@icm.edu.pl

Bibliografia

[1] CPMD. http://www.cpmd.org/. Copyright IBM Corp 1990-2008, Copyright MPI fur FestkorperforschungStuttgart 1997-2001.
[2] Geometric H/D Isotope Eﬀects and Cooperativity of the Hydrogen Bonds in Porphycene. Chem. Phys. Chem., 8: 315–321, 2007.
[3] M. Abdel-Latif, O. Kuhn. Laser control of double proton transfer in porphycenes: towards an ultrafast switch for photonic molecular wires. Theor. Chem. Acc., 128: 307–316, 2011. DOI: 10.1007/s00214-010-0847-y.
[4] A. Amadei, A.B.M. Linssen, H.J.C. Berendsen. Essential dynamics of proteins. Proteins: Structure, Function and Genetics, 17(4): 412–425, 1993.
[5] A.D. Becke. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A, 38: 3098–3100, Sep 1988.
[6] P. Bj¨orkholm, P. Daniluk, A. Kryshtafovych, K. Fidelis, R. Andersson, T.R. Hvidsten. Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics, 25(10): 1264–70, 2009.
[7] K.J. Blinowska, R. Kuś, M. Kamiński. Granger causality and information ﬂow in multivariate processes. Phys. Rev. E, 70: 050902, Nov 2004.
[8] C. Chang, T. Shen, J. Trylska, V. Tozzini, J.A. McCammon. Gated binding of ligands to HIV-1 protease:Brownian dynamics simulations in a coarse-grained model. Biophysical journal, 90(11): 3880–3885, 2006.
[9] J.R. Collins, S.K. Burt, J.W. Erickson. Flap opening in HIV-1 protease simulated by ’activated’ molecular dynamics. Nature structural biology, 2(4): 334–338, 1995.
[10] H. Cybulski, M. Pecul, T. Helgaker, M. Jaszuński. Theoretical Studies of Nuclear Magnetic Resonance Parameters for the Proton-Exchange Pathways in Porphyrin and Porphycene. J. Phys. Chem. A, 109: 4162–4171, 2005.
[11] P. Daniluk. Analysis of structural similarity of proteins using local structure descriptors [in Polish: Analiza podobieństwa struktur przestrzennych białek przy użyciu deskryptorów lokalnej struktury]. Ph.D. Thesis, University of Warsaw, 2011.
[12] P. Daniluk, B. Lesyng. A novel method to compare protein structures using local descriptors. BMC bioinformatics, 12(1): 344, 2011.
[13] J. Dobkowski, V. Galievsky, M. Gil, J. Waluk. Time-Resolved Fluorescence Studies of Porphycene Isolated in Low-Temperature Gas Matrices. Chem. Phys. Lett., 394: 410–414, 2004.
[14] J. Dobkowski, V. Galievsky, A. Starukhin, J. Waluk. Relaxation in Excited States of Porphycene in LowTemperature Argon and Nitrogen Matrices. Chem. Phys. Lett., 318: 79–84, 2000.
[15] M. Drabikowski, S. Nowakowski, J. Tiuryn. Library of local descriptors models the core of proteins accurately. Proteins, 69(3): 499–510, 2007.
[16] S. Gawinkowski, Ł. Walewski, A. Vdovin, A. Slenczka, S. Rols, M.R. Johnson, B. Lesyng, J. Waluk. Vibrations and hydrogen bonding in porphycene. Phys. Chem. Chem. Phys., 14: 5489–5503, 2012.
[17] M. Gil, J. Dobkowski, G. Wiosna-Sałyga, N. Urbańska, P. Fita, C. Radzewicz, M. Pietraszkiewicz, P. Borowicz, D. Marks, M. Glasbeek, J. Waluk. Unusual, Solvent Viscosity-Controlled Tautomerism and Photophysics: MesoAlkylated Porphycenes. J. Am. Chem. Soc., 132(38): 13472–13485, 2010.
[18] M. Gil, J. Waluk. Vibrational Gating of Double Hydrogen Tunneling in Porphycene. J. Am. Chem. Soc., 129:1335–1341, 2007.
[19] A. Górecki, M. Szypowski, M. Długosz, J. Trylska. RedMD – reduced molecular dynamics package. J. Comput. Chem., 30(14): 2364–73, 2009.
[20] A. Gorecki, J. Trylska, B. Lesyng. Causal relations in molecular dynamics from the multi-variate autoregressive model. EPL (Europhysics Letters), 75: 503, 2006.
[21] A. Gorecki, J. Trylska, B. Lesyng. Causality and correlation analyses of molecular dynamics simulation data. In From Computational Biophysics to Systems Biology (CBSB07), volume NIC Series 36, pages 25–30, Juelich, 2007. John von Neumann Institute for Computing.
[22] J. Hasegawa, K. Takata, T. Miyahara, S. Neya, M.J. Frisch, H. Nakatsuji. Excited States of Porphyrin Isomers and Porphycene Derivatives: A SAC-CI Study. J. Phys. Chem. A, 109: 3187–3200, 2005.
[23] R.W. Hockney. The potential calculation and some applications. Methods Comput. Phys., 9: 135–211, 1970.
[24] T.R. Hvidsten, A. Kryshtafovych, K. Fidelis. Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Proteins, 75(4): 870–84, 2009.
[25] T.R. Hvidsten, A. Kryshtafovych, J. Komorowski, K. Fidelis. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics, 19 Suppl. 2: ii81–91, 2003.
[26] J.M.J. Shi. Normalized cuts and image segmentation. IEEE Trans. Pattern Anal. Mach. Intell., 22(8): 888–905, 2000.
[27] M. Kaminski, K. Blinowska. A new method of the description of the information ﬂow in the brain structures. Biological Cybernetics, 65: 203–210, 1991. DOI: 10.1007/BF00198091.
[28] C.W.M. Kay, G. Elger, K. M¨obius. The Photoexcited Triplet State of Free-Base Porphycene: A Time-Resolved EPR and Electron Spin Echo Investigation. Phys. Chem. Chem. Phys., 1: 3999–4002, 1999.
[29] P.M. Kozlowski, M.Z. Zgierski, J. Baker. The Inner-Hydrogen Migration and Ground-State Structure of Porphycene. J. Chem. Phys., 109: 5905–5913, 1998.
[30] U. Langer, C. Hoelger, B. Wehrle, L. Latanowicz, E. Vogel, H.-H. Limbach. 15N NMR Study of Proton Localization and Proton Transfer Thermodynamics and Kinetics in Polycrystalline Porphycene. J. Phys. Org. Chem., 13: 23–34, 2000.
[31] C. Lee, W. Yang, R.G. Parr. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B, 37: 785–789, Jan 1988.
[32] K. Malsch, G. Hohlneicher. The Force Field of Porphycene: A Theoretical and Experimental Approach. J. Phys. Chem. A, 101: 8409–8416, 1997.
[33] K. Malsch, M. Roeb, V. Karuth, G. Hohlneicher. The Importance of Electron Correlation for the Ground State Structure of Porphycene and Tetraoxaporphyrin-Dication. Chem. Phys., 227: 331–348, 1998.
[34] G.J. Martyna, M.L. Klein, M. Tuckerman. Nos´e–Hoover chains: The canonical ensemble via continuous dynamics. J. Chem. Phys., 97(4): 2635–2643, 1992.
[35] G.J. Martyna, M.E. Tuckerman. A reciprocal space based method for treating long range interactions in ab initio and force-ﬁeld-based calculations in clusters. J. Chem. Phys., 110(6): 2810–2821, 1999.
[36] D. Marx, J. Hutter. Ab Initio Molecular Dynamics. Cambridge University Press, 2009.
[37] M. Pietrzak, M. Shibl, M. Broring, O. Kuhn, H.-H. Limbach. 1H/2H NMR Studies of Geometric H/D IsotopeEﬀects on the Coupled Hydrogen Bonds in Porphycene Derivatives. J. Am. Chem. Soc., 129: 296–304, 2007.
[38] H. Piwoński, C. Stupperich, A. Hartschuh, J. Sepioł, A. Meixner, J. Waluk. Imaging of Tautomerism in a Single Molecule. J. Am. Chem. Soc., 127: 5302–5303, 2005.
[39] J. Sepioł, Y. Stepanenko, A. Vdovin, A. Mordziński, E. Vogel, J. Waluk. Proton Tunneling in Porphycene Seeded in a Supersonic Jet. Chem. Phys. Lett., 296: 549–556, 1998.
[40] M. F. Shibl, M. Tachikawa, O. K¨uhn. The Geometric (H/D) Isotope Eﬀect in Porphycene: Grid-Based Born–Oppenheimer Vibrational Wavefunctions vs. Multi-Component Molecular Orbital Theory. Phys. Chem. Chem. Phys., 7: 1368–1373, 2005.
[41] Z. Smedarchina, M.F. Shibl, O. K¨uhn, A. Fern´andez-Ramos. The Tautomerization Dynamics of Porphycene and Its Isotopomers - Concerted Versus Stepwise Mechanisms. Chem. Phys. Lett., 436: 314–321, 2007.
[42] Z. Smith, E. Wilson, R. W. Duerst. The infrared spectrum of gaseous malonaldehyde (3-hydroxy-2-propenal). Spectrochimica Acta Part A: Molecular Spectroscopy, 39(12): 1117–1129, 1983.
[43] A. Starukhin, E. Vogel, J. Waluk. Electronic Spectra of Porphycenes in Rare Gas and Nitrogen Matrices. J. Phys. Chem. A, 102: 9999–10006, 1998.
[44] E. Steiner, P.W. Fowler. The Four-Electron Diamagnetic Ring Current of Porphycene. Org. Biomol. Chem., 1: 1785–1789, 2003.
[45] H. Strombergsson, P. Daniluk, A. Kryshtafovych, K. Fidelis, J.E. Wikberg, G.J. Kleywegt, T.R. Hvidsten. Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space. J. Chem. Inf. Model, 2008.
[46] H. Str¨ombergsson, A. Kryshtafovych, P. Prusis, K. Fidelis, J.E. Wikberg, J. Komorowski, T.R. Hvidsten. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins, 65(3): 568–79, 2006.
[47] V. Tozzini, J. Trylska, C. en Chang, J.A. McCammon. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. Journal of Structural Biology, 157(3): 606–615, 2007.
[48] N. Troullier, J.L. Martins. Eﬃcient pseudopotentials for plane-wave calculations. Phys. Rev. B, 43: 1993–2006, Jan 1991.
[49] A. Vdovin, J. Waluk, B. Dick, A. Slenczka. Mode-Selective Promotion and Isotope Eﬀects of Concerted DoubleHydrogen Tunneling in Porphycene Embedded in Superﬂuid Helium Nanodroplets. ChemPhysChem, 10(5): 761–765, 2009.
[50] J.W.F. Rowe, R.W. Duerst, E.B. Wilson. The Intramolecular Hydrogen Bond in Malonaldehyde. J. Am. Chem. Soc., 98: 4021–4023, 1976.
[51] Ł. Walewski, J. Waluk, B. Lesyng. Car-Parrinello Molecular Dynamics Study of the Intramolecular Vibrational Mode-Sensitive Double Proton-Transfer Mechanisms in Porphycene. J. Phys. Chem. A, 114: 10753–10757, 2010.
[52] J. Waluk. Ground- and Excited-State Tautomerism in Porphycenes. Acc. Chem. Res., 39: 945–952, 2006.
[53] J. Waluk. Tautomerization in Porphycenes. In Hydrogen Transfer Reactions, J.T. Hynes, J.P. Klinman, H.H. Limbach, R.L. Schowen [Eds.]. Wiley-VCH, Weinheim, 2007.
[54] J. Waluk, M. M¨uller, P. Swiderek, M. K¨ocher, E. Vogel, G. Hohlneicher, J. Michl. Electronic States of Porphycenes. J. Am. Chem. Soc., 113: 5511–5527, 1991.
[55] B. Wehrle, H.H. Limbach, M. Kocher, O. Ermer, E. Vogel. 15N-CPMAS-NMR Study of the Problem of NH Tautomerism in Crystalline Porphine and Porphycene. Angew. Chem. Int. Ed. Engl., 26: 934–936, 1987.
[56] T. Yoshikawa, S. Sugawara, T. Takayanagi, M. Shiga, M. Tachikawa. Theoretical study on the mechanism of double proton transfer in porphycene by path-integral molecular dynamics simulations. Chem. Phys. Lett., 496(1–3): 14–19, 2010.
[57] T. Yoshikawa, S. Sugawara, T. Takayanagi, M. Shiga, M. Tachikawa. Quantum tautomerization in porphycene and its isotopomers: Path-integral molecular dynamics simulations. Chemical Physics, 394(1): 46–51, 2012.

Typ dokumentu

Bibliografia

Identyfikator YADDA

bwmeta1.element.baztech-article-BPBF-0001-0005