On the physical basis of the amino acid polar requirement

Journal of Molecular Evolution

Volumn 66, Issue 5, 2008, Pages 519-528

  Mathew, Damien C ^a   Luthey Schulten, Zaida ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Genetic code; Molecular dynamics simulation; Nucleobase; Partition coefficient; Radial distribution function

Indexed keywords

AMINO ACID; DIMETHYLPYRIDINE; PYRIDINE DERIVATIVE;

AMINO ACID ANALYSIS; ARTICLE; CORRELATION COEFFICIENT; MOLECULAR DYNAMICS; PARTITION CHROMATOGRAPHY; SIMULATION;

AMINO ACIDS; ASPARTIC ACID; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENETIC CODE; LEUCINE; MODELS, MOLECULAR; NUCLEOSIDES; THERMODYNAMICS;

EID: 44249087590     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9073-9     Document Type: Article

References (33)

1. Alff-Steinberger C (1969) The genetic code and error transmission. Proc Natl Acad Sci USA 64:584-591
2. Allen M, Tildesley D (1987) Computer simulation of liquids. Clarendon Press, Oxford
3. Baaske P, Weinert FM, Duhr S, Lemke KH, Russell MJ, Braun D (2007) Extremeaccumulation of nucleotides in simulated hydrothermal pore systems. Proc Natl Acad Sci USA 104:9346-9351
4. Butler T, Goldenfeld N, Mathew D, Luthey-Schulten Z (2008) Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. arXiv:0712.3332v2[q-bio.PE]
5. Campo MG (2006) Molecular dynamics simulation of glycine zwitterion in aqueous solution. J Chem Phys 125:114511
6. Caporaso JG, Yarus M, Knight R (2005) Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. J Mol Evol 61:597-607
7. 2, CO, NO, and Xe inside myoglobin. Biophys J 91:1844-1857
8. Consden R, Gordon AH, Martin AJP (1944) Qualitative analysis of proteins: a partition chromatographic method using paper. BCHJ 38(3):224-232
9. Di Giulio M (1989) The extension reached by the minimization of the polarity distances during the evolution of the genetic code. J Mol Evol 29:288-293
10. England A, Cohn EJ (1935) Studies in the physical chemistry of amino acids, peptides and related substances in the distribution coefficients of amino acids between water and butyl alcohol. J Am Chem Soc 57:634-637
11. Ferris J, Joshi P, Wang K-J, Miyakawa S, Huang W (2004) Catalysis in prebiotic chemistry: application to the synthesis of RNA oligomers. Adv Space Res 33:100-105
12. Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47(3):238-248
13. Freeland SJ, Knight RD, Landwebber LF, Hurst LD (2000) Early fixation of an optimal genetic code. Mol Biol Evol 17(4):511-518
14. Haig D, Hurst LD (1991) A quantitative measure of error minimization in the genetic code. J Mol Evol 33:412-417
15. Huang W, Ferris JP (2003) Synthesis of 35-40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem Commun 12:1458-1459
16. Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33-38
17. Knight RD (2001) The origin and evolution of the genetic code: statistical and experimental investigations. PhD thesis, Princeton University
18. MacKerell AD Jr, Banavali N (2000) All-atom empirical force field for nucleic acids: 2. Application to molecular dynamics simulations of DNA and RNA in solution. J Comp Chem 21:105-120
19. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack R Jr, Evanseck J, Field M, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F, Mattos C, Michnick S, Ngo T, Nguyen D, Prodhom B, Reiher W III, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
20. Martin AJP, Synge RLM (1941) A new form of chromatogram employing two liquid phases. 1. A theory of chromatography. 2. Application to the micro-determination of the higher monoamino-acids in proteins. Biochem J 35:1358-1368
21. McQuarrie DA (2000) Statistical mechanics, 2nd edn. University Science Books, Sausalito, CA
22. Miller JC, Rallison JM (2007) Interfacial instability between sheared elastic liquids in a channel. J Non-Newton Fluid Mech 143:71-78
23. Mirzaev SZ, Behrends R, Heimburg T, Haller J, Kaatze U (2006a) Critical behavior of 2,6-dimethylpyridine-water: measurements of specific heat, dynamic light scattering, and shear viscosity. J Chem Phys 124:144517
24. Mirzaev SZ, Iwanowski I, Zaitdinov M, Kaatze U (2006b) Critical dynamics and kinetics of elementary reactions of 2,6-dimethylpyridine-water. Chem Phys Lett 431:308-312
25. Nigmatullin R, Lovitt R, Wright C, Linder M, Nakari-Setälä T, Gama M (2004) Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains. Colloids Surf B Biointerfaces 35:125-135
26. Nimlos MR, Matthews JF, Crowley MF, Walker RC, Chukkapalli G, Brady JW, Adney WS, Cleary JM, Zhong L, Himmel ME (2007) Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface. Protein Eng Des Sel 20:1-9
27. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781-1802
28. Sotomayor M, Vásquez V, Perozo E, Schulten K (2007) Ion conduction through MscS as determined by electrophysiology and simulation. Biophys J 92:886-902
29. Woese CR (1973) Evolution of the genetic code. Naturwissenschaften 60(10):447-459
30. Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC (1966a) On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol 31:723-736
31. Woese CR, Dugre DH, Saxinger WC, Dugre SA (1966b) The molecular basis for the genetic code. Proc Natl Acad Sci USA 55(4):966-974
32. Woese CR, Olsen GJ, Ibba M, Söoll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64:202-236
33. Yarus M, Caporaso JG, Knight R (2005) Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 74:179-198