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10.1002/prot.10195.abs Molecular dynamics simulations (MD) have been performed on variant crystal and NMR‐derived structures of the glucocorticoid receptor DNA‐binding domain (GR DBD). A loop region five residues long, the so‐called D‐box, exhibits significant flexibility, and transient...
10.1002/prot.10198.abs Pairwise contact potentials have a long, successful history in protein structure prediction. They provide an easily‐estimated representation of many attributes of protein structures, such as the hydrophobic effect. In order to improve on existing potentials, one should...
10.1002/prot.10196.abs In a similar way in which the folding of single‐domain proteins provides an important test in the study of self‐organization, the folding of homodimers constitutes a basic challenge in the quest for the mechanisms that are the basis of biological recognition....
10.1002/prot.10200.abs In zinc proteins, the Zn2+ cation frequently binds with a tetrahedral coordination to cysteine and histidine side chains, for example, in many DNA‐binding proteins, where it plays primarily a structural role. We examine the possibility of thiolate protonation in...
10.1002/prot.10177.abs Acidic pKas of histidines buried within the protein interior are frequently rationalized on the contradictory basis of either polar interactions within the protein or the effects of a hydrophobic environment. To examine these relationships, we surveyed the buried surface...
10.1002/prot.10193.abs When a denatured polypeptide is put into refolding conditions, it undergoes conformational changes on a variety of times scales. We set out here to distinguish the fast events that promote productive folding from other processes that may be generic to any non‐folding...
10.1002/prot.10199.abs Erythrocytes of the marine annelid, Glycera dibranchiata, contain a mixture of monomeric and polymeric hemoglobins. There are three major monomer hemoglobin components, II, III, IV (also called GMH2, 3, and 4), that have been highly purified and well characterized. We have...
10.1002/prot.10188.abs Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go‐like model. Force versus displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as...
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