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Journal Issue - Volume 12 Issue 10 (October 2003)

Abstract The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL‐10) consists of variable domains (Fv) and constant domains (CL–CH1). Normal modes have been calculated from the three‐dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL–Fab and HEL–Fv complexes. However, HEL–Fv had a one order of magnitude lower dissociation...

Abstract NMR residual dipolar couplings for the S‐peptide of ribonuclease A aligned in C8E5/n‐octanol liquid crystals are consistent with the presence of a native‐like α‐helix structure undergoing dynamic fraying. Residues 3–13, which correspond to the first α‐helix of ribonuclease A, show couplings that become more negative at low temperature and in the presence of salt, conditions which stabilize α‐helical structure in the S‐peptide. By...

Abstract α‐Amylases, in particular, microbial α‐amylases, are widely used in industrial processes such as starch liquefaction and pulp processes, and more recently in detergency. Due to the need for α‐amylases with high specific activity and activity at alkaline pH, which are critical parameters, for example, for the use in detergents, we have enhanced the α‐amylase from Bacillus amyloliquefaciens (BAA). The genes coding for the wild‐type BAA...

Abstract We have determined consensus protein‐fold classifications on the basis of three classification methods, SCOP, CATH, and Dali. These classifications make use of different methods of defining and categorizing protein folds that lead to different views of protein‐fold space. Pairwise comparisons of domains on the basis of their fold classifications show that much of the disagreement between the classification systems is due to...

Abstract Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle‐particle particle‐mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated...

Abstract All retroviral proteases belong to the family of aspartic proteases. They are active as homodimers, each unit contributing one catalytic aspartate to the active site dyad. An important feature of all aspartic proteases is a conserved complex scaffold of hydrogen bonds supporting the active site, called the “fireman's grip,” which involves the hydroxyl groups of two threonine (serine) residues in the active site...

Abstract Proteins are renowned for their specificity of function. There is, however, accumulating evidence that many proteins, from enzymes to antibodies, are functionally promiscuous. Promiscuity is of considerable physiological importance. In the immune system, cross‐reactive or multispecific antibodies are implicated in autoimmune and allergy conditions. In most cases, however, the mechanism behind promiscuity and the...

  • A de novo redesign of the WW domain

  • Christina M. Kraemer‐Pecore, Juliette T.J. Lecomte, John R. Desjarlais
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.03190903 (p 2194-2205)

Abstract We have used a sequence prediction algorithm and a novel sampling method to design protein sequences for the WW domain, a small β‐sheet motif. The procedure, referred to as SPANS, designs sequences to be compatible with an ensemble of closely related polypeptide backbones, mimicking the inherent flexibility of proteins. Two designed sequences (termed SPANS‐WW1 and SPANS‐WW2), using only naturally occurring l‐amino acids,...

Abstract Glycinamide ribonucleotide formyltransferases (GARTs) are part of the de novo purine biosynthetic pathway, catalyzing the direct transfer of a formyl group from the tetrahydrofolate cofactor to the glycinamide ribonucleotide substrate. Despite the low amino acid‐sequence identity between the GARTs from Escherichia coli and human, their tertiary structures are superimposable. As part of our functional studies of these enzymes, we have...

Abstract Fifteen independent 1‐nsec MD simulations of fully solvated Ca2+ saturated calmodulin (CaM) mutant D129N were performed from different initial conditions to provide a sufficient statistical basis to gauge the significance of observed dynamical properties. In all MD simulations the four Ca2+ ions remained in their binding sites, and retained a single water ligand as observed in the crystal structure. The coordination of Ca2+ ions in...

Abstract Heteronuclear NMR methods have been used to probe the conformation of four complexes of Escherichia coli dihydrofolate reductase (DHFR) in solution. 1HN, 15N, and 13Cα resonance assignments have been made for the ternary complex with folate and oxidized NADP+ cofactor and the ternary complex with folate and a reduced cofactor analog, 5,6‐dihydroNADPH. The backbone chemical shifts have been compared with those of the binary complex of DHFR with the...

Abstract Superfamily classifications are based variably on similarity of sequences, global folds, local structures, or functions. We have examined the possibility of defining superfamilies purely from the viewpoint of the global fold/function relationship. For this purpose, we first classified protein domains according to the β‐sheet topology. We then introduced the concept of kinship relations among the classified β‐sheet topology...

Abstract Staphostatins are the endogenous inhibitors of the major secreted cysteine proteases of Staphylococcus aureus, the staphopains. Here, we present the 1.4 Å crystal structure of staphostatin B and show that the fold can be described as a fully closed, highly sheared eight‐stranded β‐barrel. Thus, staphostatin B is related to β‐barrel domains that are involved in the inhibition or regulation of proteases of various catalytic types and to...

Abstract Microtubules are cylindrical polymers found in every eukaryotic cell. They have a unique helical structure that has implications at both the cellular level, in terms of the functions they perform, and at the multicellular level, such as determining the left–right symmetry in plants. Through the combination of an atomically detailed model for a microtubule and large‐scale computational techniques for computing electrostatic...

Abstract Recently we proposed a novel method of alignment–alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present several examples of the relations between PFAM protein families that were detected by COMPASS and that lead to the predictions of presently unresolved protein structures. We discuss relatively straightforward COMPASS predictions that are new...

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