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      Radius of gyration as an indicator of protein structure compactness

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      Molecular Biology
      Pleiades Publishing Ltd

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          The packing density in proteins: standard radii and volumes.

          The sizes of atomic groups are a fundamental aspect of protein structure. They are usually expressed in terms of standard sets of radii for atomic groups and of volumes for both these groups and whole residues. Atomic groups, which subsume a heavy-atom and its covalently attached hydrogen atoms into one moiety, are used because the positions of hydrogen atoms in protein structures are generally not known. We have calculated new values for the radii of atomic groups and for the volumes of atomic groups. These values should prove useful in the analysis of protein packing, protein recognition and ligand design. Our radii for atomic groups were derived from intermolecular distance calculations on a large number (approximately 30,000) of crystal structures of small organic compounds that contain the same atomic groups to those found in proteins. Our radii show significant differences to previously reported values. We also use this new radii set to determine the packing efficiency in different regions of the protein interior. This analysis shows that, if the surface water molecules are included in the calculations, the overall packing efficiency throughout the protein interior is high and fairly uniform. However, if the water structure is removed, the packing efficiency in peripheral regions of the protein interior is underestimated, by approximately 3.5 %. Copyright 1999 Academic Press.
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            How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins.

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              How do small single-domain proteins fold?

              Many small, monomeric proteins fold with simple two-state kinetics and show wide variation in folding rates, from microseconds to seconds. Thus, stable intermediates are not a prerequisite for the fast, efficient folding of proteins and may in fact be kinetic traps and slow the folding process. Using recent studies, can we begin to search for trends which may lead to a better understanding of the protein folding process?
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                Author and article information

                Journal
                Molecular Biology
                Mol Biol
                Pleiades Publishing Ltd
                0026-8933
                1608-3245
                August 2008
                August 2008
                : 42
                : 4
                : 623-628
                Article
                10.1134/S0026893308040195
                18856071
                2ca8e1fa-e42b-479d-91a7-7c466945ba39
                © 2008
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