Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins

Spassov, Velin Z.; Ladenstein, Rudolf; Karshikoff, Andrey

doi:10.1002/pro.5560060607

Cited by 32 publications

(1 citation statement)

References 27 publications

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“…Protein interiors are not simple hydrophobic environments and thus can tolerate internal charges through favorable electrostatic interactions (Spassov, Ladenstein & Karshikoff, 1997; Kim et al, 2005). Interaction with other buried charges can form stabilizing ion pairs.…”

Section: Introductionmentioning

confidence: 99%

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Gunner

Baker

2016

Methods in Enzymology

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Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.

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Section: Introductionmentioning

confidence: 99%

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Gunner

Baker

2016

Methods in Enzymology

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Role of the C-terminal chain in human interferon? stability: An electrostatic study

et al. 2001

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Influence of lysine content and PH on the stability of alanine-based copolypeptides

Vila¹,

Ripoll²,

Scheraga³

2001

Biopolymers

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To account for the relative contributions of lysine and alanine residues to the stability of α‐helices of copolymers of these two residues, conformational energy calculations were carried out for several hexadecapeptides at several pHs. All the calculations considered explicitly the coupling between the conformation of the molecule and the ionization equilibria as a function of pH. The total free energy function used in these calculations included terms that account for the solvation free energy and free energy of ionization. These terms were evaluated by means of a fast multigrid boundary element method. Reasonable agreement with experimental values was obtained for the helix contents and vicinal coupling constants (3JHNα). The helix contents were found to depend strongly on the lysine content, in agreement with recent experimental results of Williams et al. (Journal of the American Chemical Society, 1998, Vol. 120, pp. 11033–11043) In the lowest energy conformation computed for a hexadecapeptide containing 3 lysine residues at pH 6, the lysine side chains are preferentially hydrated; this decreases the hydration of the backbone CO and NH groups, thereby forcing the latter to form hydrogen bonds with each other in the helical conformation. The lowest energy conformation computed for a hexadecapeptide containing 6 lysine residues at pH 6 shows a close proximity between the NH +3 groups of the lysine side chains, a feature that was previously observed in calculations of short alanine‐based oligopeptides. The calculation on a blocked 16‐mer of alanine shows a 7% helix content based on the Boltzmann averaged vicinal coupling constants computed from the dihedral angles ϕ, consistent with previous experimental evidence on triblock copolymers containing a central block of alanines, and with earlier theoretical calculations. © 2001 John Wiley & Sons, Inc. Biopolymers 58: 235–246, 2001

show abstract

Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins

Cited by 32 publications

References 27 publications

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Role of the C-terminal chain in human interferon? stability: An electrostatic study

Influence of lysine content and PH on the stability of alanine-based copolypeptides

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