Molecular insights into the mechanisms of cation-type specific stability and denaturation of poly-l-glutamate: a simulation study

REFERENCES

• McCammonJA, WolynesPG. Current opinion in structural biology. London: Current Biology Press; 2002.
   Google Scholar
• ZhouY, KarplusM. Interpreting the folding kinetics of helical protein. Nature. 1999;401:400–403.
   Google Scholar
• SnowCD, NguyenH, PandeVS, GruebeleM. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 2002;420:102–106.
   Google Scholar
• ShenX, GuB, CheSA, ZhangFS. Solvent effects on the conformation of DNA dodecamer segment: a simulation study. J Chem Phys.2011;135:034509–034521.
   Google Scholar
• HirataF. Molecular theory of solvation. Dordrecht: Kluwer Academic Publishers; 2003.
   Google Scholar
• DebyeP, HückelE. The theory of electrolytes. I. Lowering of freezing point and related phenomena. Phys Zeits. 1923;24:185–206.
   Google Scholar
• RusselWB, SavilleDA, SchowalterWR. Colloidal dispersions. New York: Cambridge University Press; 1989.
   Google Scholar
• HansenJP, McDonaldIR. Theory of simple liquids. London: Academic Press; 1986.
   Google Scholar
• BaldwinRL. How Hofmeister ion interactions affect protein stability. Biophys J. 1996;71:2056–2063.
   Google Scholar
• CacaceMG, LandauEM, RamsdenJJ. The Hofmeister series: salt and solvent effects on interfacial phenomena. Quart Rev Biophys. 1997;30:241–277.
   Google Scholar
• KarlstromG. On the effective interaction between an ion and a hydrophobic particle in polar solvents: a step towards an understanding of the Hofmeister effect. Phys Chem Chem Phys. 2003;5:3238–3246
   Google Scholar
• MaximVF, JonathanMG, StephanS. Effects of K⁺ and Na⁺ on α-poly-L-glutamate conformations. J Am Chem Soc. 2009;131:10854–10856.
   Google Scholar
• JoachimD. Salt-specific stability and denaturation of a short salt-bridge-forming α-Helix. J Am Chem Soc. 2008;130:14000–14007.
   Google Scholar
• PerkynsJS, WangYY, PettittBM. Salting in peptides: conformationally dependent solubilities and phase behavior of a tripeptide zwitterion in electrolyte solution. J Am Chem Soc. 1996;118:1164–1172.
   Google Scholar
• HassanSA. Amino acid side chain interactions in the presence of salts. J Phys Chem B. 2005;109:21989–21996.
   Google Scholar
• GhoshT, KalraA, GardeS. On the salt-induced stabilization of pair and many-body hydrophobic interactions. J Phys Chem B. 2005;109:642–651.
   Google Scholar
• KinoshitaM, HaramoY. Potential of mean force between solute atoms in salt solution: effects due to salt species and relative conformational transition of biomelecules. Bull Chem Soc Jpn. 2005;78:1431–1441.
   Google Scholar
• ArakawaT, TimasheffSN. Abnormal solubility behavior of beta-lactoglobulin: salting-in by glycine and NaCl. Biochemistry. 1987;26:5147–5153.
   Google Scholar
• GotoY, AimotoS. Anion and pH-dependent conformational transition of an amphiphilic polypeptide. J Mol Bol. 1991;218:387–396.
   Google Scholar
• CurtisRA, UlrichJ, MontaserA, PrausnitzJM, BlanchHW. Protein–protein interactions in concentrated electrolyte solutions. Biotechnol Bioeng. 2002;79:367–380.
   Google Scholar
• KrimmS, MarkJ, TiffanyM. Influence of counterions on the helical conformations of charged polypeptide chains. Biopolymers. 1969;8:695–697.
   Google Scholar
• SatohM, KomiyamaJ, IijimaT. Dependence on ionic strength of charge-induced coil-helix transition of sodium poly(L-glutamate) in aqueous solution. Biophys Chem. 1981;14:347–355.
   Google Scholar
• Peric-HasslerL, HunenbergerPH. Interaction of alginate single-chain polyguluronate segments with mono- and divalent metal cations: a comparative molecular dynamics study. Mol Simul. 2010;36:778–795.
   Google Scholar
• LanyiJK. Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol Rev. 1974;38:272–290.
   Google Scholar
• KarplusM, McCammonJA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002;9:646–652.
   Web of Science ®Google Scholar
• YamaokaK, ResnikRA. The extrinsic cotton effect of acridine orange bound to native DNA and helical poly-α, L-glutamic acid. J Phys Chem B. 1966;70:4051–4066.
   Google Scholar
• MikhoninAV, MyshakinaNS, BykovSV, AsherSA. UV resonance Raman determination of polyproline II, extended 2.5(1)-helix, and beta-sheet psi angle energy landscape in poly-L-lysine and poly-L-glutamic acid. J Am Chem Soc. 2005;127:7712–7720.
   Google Scholar
• HolzwarthG, DotyP. The ultraviolet circular dichroism of polypeptides. J Am Chem Soc. 1965;87:218–228.
   PubMed Web of Science ®Google Scholar
• SatohM, FujiiY, KatoF, KomiyamaJ. Solvent- and salt-induced coil-helix transition of alkali metal salts of poly(l-glutamic acid) in aqueous orgnic solvents. Biopolymers. 1991;31:1–10.
   Google Scholar
• BerendenHJC, Van Der SpoelD, Van DrunenR. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun. 1995;91:43–56.
   Google Scholar
• LindahlE, HessB, Van Der SpoelD. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model. 2001;7:306–317.
   Google Scholar
• SchaftenaarG, NoordikJH. Molden: a pre- and post-processing program for molecular and electronic structures. Aided Mol Des. 2000;14:123–134.
   Google Scholar
• KaminskiGA, FriesnerRA, Tirado-RivesJ, JorgensenWL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B. 2001;28:6474–6487.
   Google Scholar
• DardenT, YorkD, PedersenL. Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Google Scholar
• NezbedaI, SlovakJ. A family of primitive models of water: three- four-, and five-site models. Mol Phys. 1997;90:353–372.
   Google Scholar
• van der SpoelD, LindahlE. Brute force molecular dynamics simulations of Villin headpiece: comparison with NMR parameters. J Phys Chem B. 2003;107:11178–11187.
   Google Scholar
• BerendsenHJC, PostmaJPM, Van GunsterenWF, DinolaA, HaakJR. Molecular-dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684–3690.
   Google Scholar
• AllenMP, TildesleyDJ. Computer simulation of liquids. New York: Oxford University Press; 1989.
   Google Scholar
• ZagrovicB, LipfertJ, SorinEJ, MillettIS, Van GunsterenWF, DoniachS, PandeVS. Unusual compactness of a polyproline type II structure. Proc Natl Acad Sci USA. 2005;102:11698–11703.
   PubMed Web of Science ®Google Scholar
• MikhoninAV, AsherSA, BykovSV, MurzaA. UV raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-Helix melting follows 3(10)-Helices and pi-Bulges premelting. J Phys Chem B. 2007;111:3280–3292.
   Google Scholar
• ZhouRH. Trp-cage: folding free energy landscape in explicit water. Proc Natl Acad Sci USA. 2003;100:13280–13285.
   PubMed Web of Science ®Google Scholar
• LubosV, PavelJ, PierreB, DidierT, WernerK. Specific ion effects at protein surfaces: A molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions. J Phys Chem B. 2008;110:7036–7043.
   Google Scholar
• VrbkaL, VondrasekJ, Jagoda-CwiklikB, VachaR, JungwirthP. Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces. Proc Natl Acad Sci USA. 2006;103:15440–15444.
   Google Scholar
• AzizEF, OttossonN, EisebittS, EberhardtW, Jagoda-CwiklikB, VachaR, JungwirthP, WinterB. Cation-specific interactions with carboxylate in amino acid and acetate aqueous s olutions: X-ray absorption and ab initio calculations. J Phys Chem B. 2008;112:12567–12570.
   Google Scholar