Insight into TPMT^∗23 mutation mis-folding using molecular dynamics simulation and protein structure analysis

References

• Barrett , C. , Hall , B.A. and Noble , M.E.M. 2004 . Dynamite: A simple way to gain insight into protein motions . Acta Crystallographica. Section D, Biological Crystallography , 60 : 2280 – 2287 .
   PubMed Web of Science ®Google Scholar
• Barrett , C. and Noble , M. 2005 . Dynamite extended: Two new services to simplify protein dynamic analysis . Bioinformatics , 21 : 3174 – 3175 .
   PubMed Web of Science ®Google Scholar
• Berk , H. , Henk , B. , Berendsen , H.J.C. and Fraaije , J.G.E.M. 1997 . LINCS: A linear constraint solver for molecular simulations . Journal of Computational Chemistry , 18 : 1463 – 1472 .
   Web of Science ®Google Scholar
• Dewit , O. , Vanheuverzwyn , R. , Desager , J.P. and Horsmans , Y. 2002 . Interaction between azathioprine and aminosalicylates: An in vivo study in patients with Crohn’s disease . Alimentary Pharmacology & Therapeutics , 16 : 79 – 85 .
   PubMed Web of Science ®Google Scholar
• Dunbrack , R.L. Jr. 2002 . Rotamer libraries in the 21st century . Current Opinion in Structural Biology , 12 : 431 – 440 .
   PubMed Web of Science ®Google Scholar
• Hess , B. , Kutzner , C. , Van der Spoel , D. and Lindahl , E. 2008 . GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation . Journal of Chemical Theory and Computation , 4 : 435 – 447 .
   PubMed Web of Science ®Google Scholar
• Humphrey , W. , Dalke , A. and Schulten , K. 1996 . VMD: Visual molecular dynamics . Journal of Molecular Graphics , 14 ( 33–38 ) : 27 – 38 .
   Google Scholar
• Hünenberger , P.H. 2005 . Thermostat algorithms for molecular dynamics simulations . Advances in Polymer Science , 173 : 105 – 149 .
   Web of Science ®Google Scholar
• Idiong , G. , Won , A. , Ruscito , A. , Leung , B.O. , Hitchcock , A.P. and Ianoul , A. 2011 . Investigating the effect of a single glycine to alanine substitution on interactions of antimicrobial peptide latarcin 2a with a lipid membrane . European Biophysics Journal , 40 : 1087 – 1100 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W.L. , Maxwell , D.S. and Tirado-Rives , J. 1996 . Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids . Journal of the American Chemical Society , 118 : 11225 – 11236 .
   Web of Science ®Google Scholar
• Kaminski , G.A. , Friesner , R.A. , Tirado-Rives , J. and Jorgensen , W.L. 2001 . Evaluation and reparametrization of the opls-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides . Journal of Physical Chemistry B , 105 : 6474 – 6487 .
   Web of Science ®Google Scholar
• Kersti , O. and Kaili , A. 2007 . Inhibition of human thiopurine S-methyltransferase by various nonsteroidal anti-inflammatory drugs in vitro: A mechanism for possible drug interactions . Drug Metabolism and Disposition , 35 : 1452 – 1454 .
   PubMed Web of Science ®Google Scholar
• Kröplin , T. , Fischer , C. and Iven , H. 1999 . Inhibition of thiopurine S-methyltransferase activity by impurities in commercially available substrates: A factor for differing results of TPMT measurements . European Journal of Clinical Pharmacology , 55 : 285 – 291 .
   PubMed Web of Science ®Google Scholar
• Kumar , P. , Henikoff , S. and Ng , P.C. 2009 . Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm . Nature Protocols , 4 : 1073 – 1081 .
   PubMed Web of Science ®Google Scholar
• Kutzner, C., Van der Spoel, D., Fechner, M., Lindahl, E., Schmitt, U.W., De Groot, B.L., & Grubmüller, H. (2006). Improved GROMACS scaling on Ethernet switched clusters. Recent advances in parallel virtual machine and message passing interface. Lecture Notes in Computer Science, 4192. Berlin: Springer, 404–405.
   Google Scholar
• Kutzner , C. , Van der Spoel , D. , Fechner , M. , Lindahl , E. , Schmitt , U.W. , De Groot , B.L. and Grubmüller , H. 2007 . Speeding up parallel GROMACS on high-latency networks . Journal of Computational Chemistry , 28 : 2075 – 2084 .
   PubMed Web of Science ®Google Scholar
• Lindahl , E. , Hess , B. and Van der Spoel , D. 2001 . GROMACS 3.0: A package for molecular simulation and trajectory analysis . Journal of Molecular Modeling , 7 : 306 – 317 .
   Web of Science ®Google Scholar
• Lindqvist , M. , Skoglund , K. , Karlgren , A. , Söderkvist , P. , Peterson , C. , Kidhall , I. and Almer , S. 2007 . Explaining TPMT genotype/phenotype discrepancy by haplotyping of TPMT∗3A and identification of a novel sequence variant, TPMT∗23 . Pharmacogenetics and Genomics , 17 : 891 – 895 .
   PubMed Web of Science ®Google Scholar
• López-Llano , J. , Campos , L.A. and Sancho , J. 2006 . Alpha-helix stabilization by alanine relative to glycine: Roles of polar and apolar solvent exposures and of backbone entropy . Proteins , 64 : 769 – 778 .
   PubMed Web of Science ®Google Scholar
• Mokmak , W. , Tongsima , S. and Jenwitheesuk , E. 2009 . Molecular dynamics simulation of a human thiopurine S-methyltransferase complexed with 6-mercaptopurine model . Bioinformation , 4 : 59 – 62 .
   PubMedGoogle Scholar
• Ng , P.C. and Henikoff , S. 2001 . Predicting deleterious amino acid substitutions . Genome Research , 11 : 863 – 874 .
   PubMed Web of Science ®Google Scholar
• Ng , P.C. and Henikoff , S. 2002 . Accounting for human polymorphisms predicted to affect protein function . Genome Research , 12 : 436 – 446 .
   PubMed Web of Science ®Google Scholar
• Ng , P.C. and Henikoff , S. 2003 . SIFT: Predicting amino acid changes that affect protein function . Nucleic Acids Research , 31 : 3812 – 3814 .
   PubMed Web of Science ®Google Scholar
• Ng , P.C. and Henikoff , S. 2006 . Predicting the effects of amino acid substitutions on protein function . Annual Review of Genomics and Human Genetics , 7 : 61 – 80 .
   PubMed Web of Science ®Google Scholar
• Nosé , S. and Klein , M.L. 1983 . Constant pressure molecular dynamics for molecular systems . Molecular Physics , 50 : 1055 – 1076 .
   Web of Science ®Google Scholar
• Pazmiño , P.A. , Sladek , S.L. and Weinshilboum , R.M. 1980 . Thiol S-methylation in uremia: Erythrocyte enzyme activities and plasma inhibitors . Clinical Pharmacology and Therapeutics , 28 : 356 – 367 .
   PubMed Web of Science ®Google Scholar
• Rutherford , K. and Daggett , V. 2008 . Four human thiopurine S-methyltransferase alleles severely affect protein structure and dynamics . Journal of Molecular Biology , 379 : 803 – 814 .
   PubMed Web of Science ®Google Scholar
• Serrano , L. , Neira , J.L. , Sancho , J. and Fersht , A.R. 1992 . Effect of alanine versus glycine in alpha-helices on protein stability . Nature , 356 : 453 – 455 .
   PubMed Web of Science ®Google Scholar
• Tai , K. , Shen , T. , Henchman , R.H. , Bourne , Y. and Marchot , P. 2002 . Mechanism of acetylcholinesterase inhibition by fasciculin: A 5 ns molecular dynamics simulation . Journal of the American Chemical Society , 124 : 6153 – 6161 .
   PubMed Web of Science ®Google Scholar
• Ujiie , S. , Sasaki , T. , Mizugaki , M. , Ishikawa , M. and Hiratsuka , M. 2008 . Functional characterization of 23 allelic variants of thiopurine S-methyltransferase gene (TPMT∗2–∗24) . Pharmacogenetics and Genomics , 18 : 887 – 893 .
   PubMed Web of Science ®Google Scholar
• Ulrich , E. , Lalith , P. , Berkowitz , Max L. , Tom , D. , Hsing , L. and Pedersen Lee , G. 1995 . A smooth particle mesh Ewald method . The Journal of Chemical Physics , 103 : 8577 – 8593 .
   Web of Science ®Google Scholar
• Wu , H. , Horton , J.R. , Battaile , K. , Allali-Hassani , A. , Martin , F. , Zeng , H. , Loppnau , P. , Vedadi , M. , Bochkarev , A. , Plotnikov , A.N. and Cheng , X. 2007 . Structural basis of allele variation of human thiopurine-S-methyltransferase . Proteins , 67 : 198 – 208 .
   PubMed Web of Science ®Google Scholar