A systematic analysis of buried polar side chains and their interactions in α-helical proteins

MS Kondratova, AV Efimov - Molecular Biology, 2002 - Springer
MS Kondratova, AV Efimov
Molecular Biology, 2002Springer
Examination of 80 α-helical proteins and domains demonstrates that they contain from 1 to
more than 20 completely buried (water-inaccessible) polar side chains. As a rule the latter
have partners for H-bonding but the resulting H-bond system is often not saturating. Basing
on statistical analysis, we determined the optimal number of H-bonds for every type of polar
side chain, and discuss the structural role of vacant donors and acceptors. About half of the
H-bonds formed by buried side chains pertain to interhelix contacts of the (side chain)–(side …
Abstract
Examination of 80 α-helical proteins and domains demonstrates that they contain from 1 to more than 20 completely buried (water-inaccessible) polar side chains. As a rule the latter have partners for H-bonding but the resulting H-bond system is often not saturating. Basing on statistical analysis, we determined the optimal number of H-bonds for every type of polar side chain, and discuss the structural role of vacant donors and acceptors. About half of the H-bonds formed by buried side chains pertain to interhelix contacts of the (side chain)–(side chain) and (side chain)–(main chain) types. Such interactions appear to be a most important factor determining the mutual arrangement of α-helices in proteins. Analysis of the frequency of occurrence of various interacting pairs reveals that these interactions are selective.
Springer
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