The effect of a Pro28Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study

Journal of Molecular Modeling

Volumn 17, Issue 10, 2011, Pages 2639-2649

  Jójárt, Balázs ^a   Szori, Milán ^a   Izsák, Róbert ^a   Marsi, István ^a   László, Aranka ^b   Csizmadia, Imre G ^a,c   Viskolcz, Béla ^a  

^a UNIVERSITY OF SZEGED   (Hungary)

^b UNIVERSITY OF SZEGED   (Hungary)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

sheet stability; AIM; Human galactokinase; Local unfolding; MMPBSA GBSA; Molecular dynamics

Indexed keywords

AMINO ACID; GALACTOKINASE; HYDROGEN; PROLYL 28 THREONINE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARTICLE; BETA SHEET; BINDING KINETICS; ENZYME STABILITY; ENZYME STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; POINT MUTATION; PRIORITY JOURNAL; PROTEIN UNFOLDING; AMINO ACID SUBSTITUTION; CHEMISTRY; GENETICS; HUMAN; PROTEIN CONFORMATION;

AMINO ACID SUBSTITUTION; ENZYME STABILITY; GALACTOKINASE; HUMANS; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; POINT MUTATION; PROTEIN CONFORMATION;

EID: 80255126249     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-0958-y     Document Type: Article

References (42)

1. AJ Bordner RA Abagyan 2004 Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations Proteins Struct Func Bioinf 57 400 413 10.1002/prot.20185 1:CAS:528:DC%2BD2cXnvFars70%3D (Pubitemid 39223745)
2. D Gilis M Rooman 1999 Prediction of stability changes upon single-site mutations using database-derived potentials Theor Chem Acc 101 46 50 1:CAS:528:DyaK1MXit1Smtbs%3D
3. P Carlsson KF Koehler L Nilsson 2005 Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization Mol Endocrinol 19 1960 1977 10.1210/me.2004-0203 1:CAS:528:DC%2BD2MXmvV2jurs%3D (Pubitemid 41124195)
4. SF Sneddon DJ Tobias 1992 The role of packing interactions in stabilizing folded proteins Biochemistry 31 2842 2846 10.1021/bi00125a028 1:CAS:528:DyaK38Xht1emsL0%3D
5. LX Dang KM Merz PA Kollman 1989 Free-energy calculations on protein stability: Thr-1573Val-157 mutation of T4 lysozyme J Am Chem Soc 111 8505 8508 10.1021/ja00204a027 1:CAS:528:DyaL1MXlslSmsb8%3D (Pubitemid 19269282)
6. S Piana A Laio F Marinelli M Van Troys D Bourry Ch Ampe JC Martins 2008 Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants J Mol Biol 375 460 470 10.1016/j.jmb.2007.10.020 1:CAS:528:DC%2BD2sXhsVWjsrjP (Pubitemid 350192477)
7. MA Sahai B Viskolcz EF Pai IG Csizmadia 2007 Quantifying the intrinsic effects of two point mutation models of proline proline diamino acid diamide: a first-principle computational study J Phys Chem B 111 11592 11602 10.1021/jp073471h 1:CAS:528:DC%2BD2sXhtVSgs7bM (Pubitemid 47598342)
8. R Gitzelmann RG Hansen 1974 Galactose biogenesis and disposal in galactosemics Biochim Biophys Acta 372 374 378 1:CAS:528:DyaE2MXntFWqtA%3D%3D
9. HM Holden JB Thoden DJ Timson RJ Reece 2004 Galactokinase: structure, function and role in type II galactosemia Cell Mol Life Sci 61 2471 2484 10.1007/s00018-004-4160-6 1:CAS:528:DC%2BD2cXhtVOmt7nO (Pubitemid 39586512)
10. JH Kinoshita E Dikmak K Satoh L Merola 1962 Osmotic changes caused by accumulation of dulcitol in lenses of rats fed With galactose Nature 194 1085 1087 10.1038/1941085a0 1:CAS:528:DyaF38Xktlygsb4%3D
11. S Tsakiris KH Schulpis K Marinou P Behrakis 2004 Protective effect of l-cysteine and glutathione on the modulated suckling rat brain Na+, K+ ATPase and Mg2+ ATPase activities induced by the in vitro galactosaemia Pharmacol Res 49 475 479 10.1016/j.phrs.2003.11.006 1:CAS:528:DC%2BD2cXhsleqt7k%3D (Pubitemid 38283869)
12. JB Thoden DJ Timson RJ Reece HM Holden 2005 Molecular structure of human galactokinase-implications for type II galactosemia J Biol Chem 280 9662 9670 10.1074/jbc.M412916200 1:CAS:528:DC%2BD2MXitVChsLk%3D (Pubitemid 40409664)
13. DJ Timson RJ Reece 2003 Functional analysis of disease-causing mutations in human galactokinase Eur J Biochem 270 1767 1774 10.1046/j.1432-1033.2003. 03538.x 1:CAS:528:DC%2BD3sXjtl2ju7w%3D (Pubitemid 36532535)
14. Nowicka A, Mackiewicz P, Dudkiewicz M, Mackiewicz D, Kowalczuk M, Cebrat S, Dudek MR (2003) In: Sloot PMA, et al. (eds) Correlation between mutation pressure, selection pressure, and occurrence of amino acids. ICCS, LNCS 2658:650-657
15. LV Kalaydjieva A Perez-Lezaun D Angelicheva S Onengut D Dye NU Bosshard A Jordanova A Savov P Yanakiev I Kremensky B Radeva J Hallmayer A Markov V Nedkova I Tournev L Aneva R Gitzelmann 1999 A founder mutation in the GK1 gene is responsible for galactokinase deficiency in Roma (Gypsies) Am J Hum Genet 65 1299 1307 10.1086/302611 1:CAS:528:DyaK1MXns1Clur0%3D (Pubitemid 30460380)
16. M Hunter E Heyer F Austerlitz D Angelicheva V Nedkova P Briones A Gata R De Pablo A Laszlo L Bosshard R Gitzelmann A Tordai L Kalmar C Szalai I Balogh C Lupu A Corches G Popa A Perez-Lezaun LV Kalaydjieva 2002 The P28 mutation in the GALK1 gene accounts for galactokinase deficiency in Roma (Gypsy) patients across Europe Pediatr Res 51 602 606 10.1203/00006450-200205000-00010 1:CAS:528:DC%2BD38XjvFeltrw%3D (Pubitemid 34453577)
17. E Capriotti P Fariselli R Casadio 2005 I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure Nucleic Acids Res 33 W306 W310 10.1093/nar/gki375 1:CAS:528:DC%2BD2MXlslyrtLY%3D (Pubitemid 44529932)
18. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The Protein Data Bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 1:CAS:528:DC%2BD3cXhvVKjt7w%3D (Pubitemid 30047768)
19. H Berman K Henrick H Nakamura 2003 Announcing the Worldwide Protein Data Bank Nat Struct Biol 10 980 10.1038/nsb1203-980 1:CAS:528:DC%2BD3sXptFOmsbY%3D (Pubitemid 37500485)
20. Molecular Operating Environment (2007) C.C.G. Inc, Montreal, Quebec, Canada
21. TJ Dolinsky JE Nielsen JA McCammon NA Baker 2004 Pdb2Pqr: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res 32 W665 W667 10.1093/nar/gkh381 1:CAS:528:DC%2BD2cXlvFKmsbY%3D (Pubitemid 38997419)
22. WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 Comparison of Simple Potential Functions for Simulating Liquid Water J Chem Phys 79 926 935 10.1063/1.445869 1:CAS:528:DyaL3sXksF2htL4%3D
23. A MacKerell D Bashford M Bellott RL Dunbrack JD Evanseck MJ Field S Fischer J Gao H Guo S Ha D Joseph-McCarthy L Kuchnir K Kuczera FTK Lau C Mattos S Michnick T Ngo DT Nguyen B Prodhom WE Reiher B Roux M Schlenkrich JC Smith R Stote J Straub M Watanabe J Wiorkiewicz-Kuczera D Yin M Karplus 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B 102 3586 3616 10.1021/jp973084f 1:CAS:528:DyaK1cXivVOlsb4%3D (Pubitemid 128576688)
24. AD Mackerell M Feig CL Brooks 2004 Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J Comput Chem 25 1400 1415 10.1002/jcc.20065 1:CAS:528: DC%2BD2cXlsVOgt7c%3D
25. D Beglov B Roux 1994 Finite representation of an infinite bulk system-solvent boundary potential for computer-simulations J Chem Phys 100 9050 9063 10.1063/1.466711 1:CAS:528:DyaK2cXkvFaqtbY%3D
26. Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06
27. HJC Berendsen JPM Postma WF Van Gunsteren A Dinola JR Haak 1984 Molecular dynamics with coupling to an external bath J Chem Phys 81 3684 3690 10.1063/1.448118 1:CAS:528:DyaL2cXmtlGksbY%3D
28. T Darden D York L Pedersen 1993 Particle mesh Ewald-an N∈×∈Log(N) method for Ewald sums in large systems J Chem Phys 98 10089 10092 10.1063/1.464397 1:CAS:528:DyaK3sXks1Ohsr0%3D
29. LSD Caves JD Evanseck M Karplus 1998 Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin Protein Sci 7 649 666 1:CAS:528:DyaK1cXhvV2lu7k%3D (Pubitemid 28130887)
30. GA Kaminski RA Friesner J Tirado-Rives WL Jorgensen 2001 Evaluation and reparametrization of the OPLS-AA force field forpProteins via comparison with accurate quantum chemical calculations on peptides J Phys Chem B 105 6474 6487 10.1021/jp003919d 1:CAS:528:DC%2BD3MXislKhsLk%3D (Pubitemid 35339015)
31. RFW Bader 1985 Atoms in molecules Acc Chem Res 18 9 15 10.1021/ar00109a003 1:CAS:528:DyaL2MXmtFGgsA%3D%3D
32. RFW Bader 1991 A quantum-theory of molecular-structure and its applications Chem Rev 91 893 928 10.1021/cr00005a013 1:CAS:528: DyaK3MXkvFWgt7s%3D
33. J Srinivasan TE Cheatham P Cieplak PA Kollman DA Case 1998 Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices J Am Chem Soc 120 9401 9409 10.1021/ja981844+ 1:CAS:528:DyaK1cXlsVyqtLo%3D (Pubitemid 28452628)
34. PA Kollman I Massova C Reyes B Kuhn S Huo L Chong M Lee T Lee Y Duan W Wang O Donini P Cieplak J Srinivasan DA Case TE Cheatham III 2000 Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc Chem Res 33 889 897 10.1021/ar000033j 1:CAS:528:DC%2BD3cXmvFGiu7g%3D (Pubitemid 32056774)
35. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco
36. BR Brooks D Janežič M Karplus 1995 Harmonic analysis of large system. I. Methodology J Comput Chem 16 1522 1542 10.1002/jcc.540161209 1:CAS:528:DyaK2MXpsVGmtbk%3D
37. W Humphrey A Dalke K Schulten 1996 VMD: Visual molecular dynamics J Mol Graph 14 33 38 10.1016/0263-7855(96)00018-5 1:CAS:528:DyaK28Xis12nsrg%3D (Pubitemid 26152973)
38. W Kabsch C Sander 1983 Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features Biopolymers 22 2577 2637 10.1002/bip.360221211 1:CAS:528:DyaL2cXkslegtQ%3D%3D
39. M Mezei 2010 Simulaid: a simulation facilitator and analysis program J Comput Chem 31 2658 2668 10.1002/jcc.21551 1:CAS:528:DC%2BC3cXhtVyitbbF
40. DJ Tobias SF Sneddon CL Brooks 1992 Stability of a model beta-sheet in water J Mol Biol 227 1244 1252 10.1016/0022-2836(92)90534-Q 1:CAS:528: DyaK3sXis1Kj
41. SF Sneddon DJ Tobias CL Brooks 1989 Thermodynamics of amide hydrogen-bond formation in polar and apolar solvents J Mol Biol 209 817 820 10.1016/0022-2836(89)90609-8 1:CAS:528:DyaK3cXhtVKitbk%3D (Pubitemid 20046134)
42. A Seshasayee 2005 High-temperature unfolding of a Trp-cage mini-protein: a molecular dynamics simulation study Theor Biol Med Model 2 7 11 10.1186/1742-4682-2-7 (Pubitemid 40605306)