2012
DOI: 10.1021/ct300492n
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Effects of Lysine Substitution on Stability of Polyalanine α Helix

Abstract: We have studied stability of polyalanine alpha-helices with lysine residues added at C-and N-termini in gas-phase and aqueous solution. Monte Carlo simulations with the fixed-charges OPLS-AA and our polarizable POSSIM force fields were carried out. The results of the simulations confirm previously observed phenomena of the helix being stable with the LYS residue on the C-terminus and losing its helical structure if the charged LYS residue is located at the N-terminus of the polypeptide in gas-hase. Both OPLS-A… Show more

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Cited by 8 publications
(21 citation statements)
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“…12 These parametrizations were carried out using the structures shown in Figure 6 for the charged termini and analogous ones for the electrostatically neutral termini. These fragments correspond to the termini with an adjacent alanine residue.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…12 These parametrizations were carried out using the structures shown in Figure 6 for the charged termini and analogous ones for the electrostatically neutral termini. These fragments correspond to the termini with an adjacent alanine residue.…”
Section: Resultsmentioning
confidence: 99%
“…12 Following this success, we have now extended the development of the POSSIM force field to the complete set of amino acids and applied it in test simulations of a collagen-like protein. The results are presented in this article.…”
Section: Introductionmentioning
confidence: 99%
“…Most of the POSSIM parameters for the p K a calculations of acid and basic residues of OMTKY3 protein were adopted from previous works . New parameters were produced whenever they did not exist before.…”
Section: Resultsmentioning
confidence: 99%
“…These calculations are done with modified POSSIM software suite including revised FB continuum solvation model. POSSIM force field was used for simulating the solutes in the p K a calculations of both the acid and the base residues of OMTKY3 protein. Values of the hydration parameters of the small molecules were produced by fitting to the experimental or quantum mechanical solvation energies of these systems.…”
Section: Resultsmentioning
confidence: 99%
“…The formalisms of the fixed‐charges OPLS‐AA and our polarizable POSSIM force fields can be described briefly as follows. The total energy E tot is found as a sum of the electrostatic interactions E electrostatic , the van‐der‐Waals energy E vdW , harmonic bond stretching and angle bending E stretch and E bend , and the torsional energy E torsion : Etot=Eelectrostatic+EvdW+Estretch+Ebend+Etorsion …”
Section: Methodsmentioning
confidence: 99%