Do salt bridges stabilize proteins? A continuum electrostatic analysis
نویسندگان
چکیده
منابع مشابه
Continuum Electrostatic Analysis of Proteins
Electrostatic interactions play an important role in many biochemical systems especially because of their long range. Electrostatic interactions often guide the association of binding partners, but they also tune catalytic properties of the active site of enzymes. For instance, the protonation and redox behavior of residues and prostetic groups in protein is heavily influenced by the electrosta...
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We estimate the free energies of transfer of ionized amino acid side chains in water to both their ion-paired and neutral hydrogen-bonded states in low-dielectric media. The difference between the two free energies corresponds to the proton transfer free energy in a "salt bridge" formed between acidic and basic groups (i.e., lysine and glutamic acid residues). Our approach is to use gas phase p...
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UNLABELLED Salt bridges can play important roles in protein structure and function and have stabilizing and destabilizing effects in protein folding. ESBRI is a software available as web tool which analyses the salt bridges in a protein structure, starting from the atomic coordinates. In the case of protein complexes, the salt bridges between protein chains can be evaluated, as well as those am...
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We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex,...
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To understand water-protein interactions in solution, the electrostatic field is calculated by solving the Poisson-Boltzmann equation, and the free energy surface of water is mapped by translating and rotating an explicit water molecule around the protein. The calculation is applied to T4 lysozyme with data available on the conservation of solvent binding sites in 18 crystallographically indepe...
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ژورنال
عنوان ژورنال: Protein Science
سال: 1994
ISSN: 0961-8368
DOI: 10.1002/pro.5560030206