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Journal Issue - Volume 14 Issue 3 (March 2005)

Abstract Human γD‐crystallin (HγD‐Crys) is a monomeric eye lens protein composed of two highly homologous β‐sheet domains. The domains interact through interdomain side chain contacts forming two structurally distinct regions, a central hydrophobic cluster and peripheral residues. The hydrophobic cluster contains Met43, Phe56, and Ile81 from the N‐terminal domain (N‐td) and Val132, Leu145, and Val170 from the C‐terminal domain...

Abstract Solubility of proteins on overexpression in Escherichia coli is a manifestation of the net effect of several sequence‐dependent and sequence‐independent factors. This study aims to delineate the relationship between the primary structure and solubility on overexpression. The amino acid sequences of proteins reported to be soluble or to form inclusion bodies on overexpression in E. coli under normal growth conditions were analyzed. The...

Abstract β‐Amyloid (Aβ) is a major protein component of senile plaques in Alzheimer's disease, and is neurotoxic when aggregated. The size of aggregated Aβ responsible for the observed neurotoxicity and the mechanism of aggregation are still under investigation; however, prevention of Aβ aggregation still holds promise as a means to reduce Aβ neurotoxicity. In research presented here, we show that Hsp20, a novel α‐crystallin...

Abstract Much attention is being paid to protein databases as an important information source for proteome research. Although used extensively for similarity searches, protein databases themselves have not fully been characterized. In a systematic attempt to reveal protein‐database characters that could contribute to revealing how protein chains are constructed, frequency distributions of all possible combinatorial sets of three,...

Abstract Amide hydrogen exchange (HX) in combination with mass spectrometry (MS) is a powerful tool to analyze the folding and dynamics of proteins. In the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. Some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform HX at shorter time intervals...

Abstract We carry out an extensive statistical study of the applicability of normal modes to the prediction of mobile regions in proteins. In particular, we assess the degree to which the observed motions found in a comprehensive data set of 377 nonredundant motions can be modeled by a single normal‐mode vibration. We describe each motion in our data set by vectors connecting corresponding atoms in two crystallographically known...

Abstract The C‐terminal region of focal adhesion kinase (FAK) consists of a right‐turn, elongated, four‐helix bundle termed the focal adhesion targeting (FAT) domain. The structure of this domain is maintained by hydrophobic interactions, and this domain is also the proposed binding site for the focal adhesion protein paxillin. Paxillin contains five well‐conserved LD motifs, which have been implicated in the binding of many focal...

Abstract Two‐chain aggregation simulations using minimalist models of proteins G, L, and mutants were used to investigate the fundamentals of protein aggregation. Mutations were selected to break up repeats of hydrophobic beads in the sequence while maintaining native topology and folding ability. Data are collected under conditions in which all chain types have similar folded populations and after equilibrating the separated chains...

Abstract The crystal structures of calcium‐loaded apoaequorin and apo‐obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF‐hand loops that have the canonical calcium‐binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium‐loaded apo‐proteins retain the same compact scaffold and overall fold as the...

Abstract The recombinant expression of integral membrane proteins is considered a major challenge, and together with the crystallization step, the major hurdle toward routine structure determination of membrane proteins. Basic methodologies for high‐throughput (HTP) expression optimization of soluble proteins have recently emerged, providing statistically significant success rates for producing such proteins. Experimental procedures...

Abstract Protein pin array technology was used to identify subunit–subunit interaction sites in the small heat shock protein (sHSP) αB crystallin. Subunit–subunit interaction sites were defined as consensus sequences that interacted with both human αA crystallin and αB crystallin. The human αB crystallin protein pin array consisted of contiguous and overlapping peptides, eight amino acids in length, immobilized on pins that were in...

Abstract It has been claimed that β2‐microglobulin (β2‐m) interacts with type I and type II collagen, and this property has been linked to the tissue specificity of the β2‐m amyloid deposits that target the osteo‐articular system. The binding parameters of the interaction between collagen and β2‐m were determined by band shift electrophoresis and surface plasma resonance by using bovine collagen of type I and type II and various...

Abstract We tested the Binding Threshold Hypothesis (BTH) for activation of olfactory receptors (ORs): To activate an OR, the odorant must bind to the OR with binding energy above some threshold value. The olfactory receptor (OR) 912‐93 is known experimentally to be activated by ketones in mouse, but is inactive to ketones in human, despite an amino acid sequence identity of ∼66%. To investigate the origins of this difference, we...

Abstract Identification of protein biochemical functions based on their three‐dimensional structures is now required in the post–genome‐sequencing era. Ligand binding is one of the major biochemical functions of proteins, and thus the identification of ligands and their binding sites is the starting point for the function identification. Previously we reported our first trial on structure‐based function prediction, based on the...

Abstract Appr‐1″‐pase, an important and ubiquitous cellular processing enzyme involved in the tRNA splicing pathway, catalyzes the conversion of ADP‐ribose‐1″monophosphate (Appr‐1″‐p) to ADP‐ribose. The structures of the native enzyme from the yeast and its complex with ADP‐ribose were determined to 1.9 Å and 2.05 Å, respectively. Analysis of the three‐dimensional structure of this protein, selected as a target in a structural...

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