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Journal Issue - Volume 12 Issue 12 (December 2003)

Abstract A comparison of the contributions and position dependence of cross‐strand electrostatic and aromatic side‐chain interactions to β‐sheet stability has been performed by using nuclear magnetic resonance in a well‐folded β‐hairpin peptide of the general sequence XRTVXVdPGOXITQX. Phe–Phe and Glu–Lys pairs were varied at the internal and terminal non–hydrogen‐bonded position, and the resulting stability was measured by the...

Abstract Human respiratory syncytial virus (RSV) encodes a small hydrophobic (SH) protein, whose function in the life cycle of the virus is unknown. Recent channel activity measurements of the protein suggest that like other viroporins, SH may assemble into a homo‐oligomeric ion channel. To further our understanding of this potentially important protein, a new strategy was implemented in order to model the transmembrane oligomeric...

Abstract A combined molecular dynamics simulation and multiple ligand docking approach is applied to study the roles of the anionic subsite residues (W86, E202, Y337) in the binding of acetylcholine (ACh) to acetylcholinesterase (AChE). We find that E202 stabilizes docking of ACh via electrostatic interactions. However, we find no significant electrostatic contribution from the aromatic residues. Docking energies of ACh to mutant...

Abstract The nuclear poly(A) binding protein (PABPN1) stimulates poly(A) polymerase and controls the lengths of poly(A) tails during pre‐mRNA processing. The wild‐type protein possesses 10 consecutive Ala residues immediately after the start methionine. Trinucleotide expansions in the coding sequence result in an extension of the Ala stretch to maximal 17 Ala residues in total. Individuals carrying the trinucleotide expansions...

Abstract The heat‐induced denaturation kinetics of two different sources of ovalbumin at pH 7 was studied by chromatography and differential scanning calorimetry. The kinetics was found to be independent of protein concentration and salt concentration, but was strongly dependent on temperature. For highly pure ovalbumin, the decrease in nondenatured native protein showed first‐order dependence. The activation energy obtained with...

Abstract An alternative core packing group, involving a set of five positions, has been introduced into human acidic FGF‐1. This alternative group was designed so as to constrain the primary structure within the core region to the same threefold symmetry present in the tertiary structure of the protein fold (the β‐trefoil superfold). The alternative core is essentially indistinguishable from the WT core with regard to structure,...

Abstract We analyze packing imperfections in globular proteins as reflected in deviations of torsion angles from the equilibrium values for the isolated side chains. The distribution of conformations of methionine and lysine residues in a database of high‐resolution structures is compared with energies of model compounds calculated with high‐level quantum‐mechanics. The distribution of the C–C and C–S torsion angles (χ3) correlates...

Abstract The tailspike protein from the bacteriophage P22 is a well characterized model system for folding and assembly of multimeric proteins. Folding intermediates from both the in vivo and in vitro pathways have been identified, and both the initial folding steps and the protrimer‐to‐trimer transition have been well studied. In contrast, there has been little experimental evidence to describe the assembly of the protrimer....

Abstract Here we report the successful three‐dimensional crystallization of GlpT, the glycerol‐3‐phosphate transporter from Escherichia coli inner membrane. GlpT possesses 12 transmembrane α‐helices and is a member of the major facilitator superfamily. It mediates the exchange of glycerol‐3‐phosphate for inorganic phosphate across the membrane. Approximately 20 phospholipid molecules per protein, identified as negatively charged...

Abstract The NS3 helicase of the hepatitis C virus (HCV) unwinds double‐stranded (ds) nucleic acid (NA) in an NTP‐dependent fashion. Mechanistic details of this process are, however, largely unknown for the HCV helicase. We have studied the binding of dsDNA to an engineered version of subdomain 2 of the HCV helicase (d2ΔNS3h) by NMR and circular dichroism. Binding of dsDNA to d2ΔNS3h induces a local unfolding of helix (α3), which includes...

Abstract A fundamental understanding of protein stability and the mechanism of denaturant action must ultimately rest on detailed knowledge about the structure, solvation, and energetics of the denatured state. Here, we use 17O and 2H magnetic relaxation dispersion (MRD) to study urea‐induced denaturation of intestinal fatty acid‐binding protein (I‐FABP). MRD is among the few methods that can provide molecular‐level information about protein...

Abstract As part of a program to discover improved glycoside hydrolase family 12 (GH 12) endoglucanases, we have extended our previous work on the structural and biochemical diversity of GH 12 homologs to include the most stable fungal GH 12 found, Humicola grisea Cel12A. The H. grisea enzyme was much more stable to irreversible thermal denaturation than the Trichoderma reesei enzyme. It had an apparent denaturation midpoint (Tm) of 68.7°C, 14.3°C higher...

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Abstract HAMLET (human α‐lactalbumin made lethal to tumor cells) is a complex of human α‐lactalbumin and oleic acid (C18:1:9 cis) that kills tumor cells by an apoptosis‐like mechanism. Previous studies have shown that a conformational change is required to form HAMLET from α‐lactalbumin, and that a partially unfolded conformation is maintained in the HAMLET complex. This study examined if unfolding of α‐lactalbumin is sufficient to...

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Abstract Proteins can adjust their structure and function in response to shifting environments. Functional diversity is created not only by the sequence but by changes in tertiary structure. Here we present evidence that lipid cofactors may enable otherwise unstable protein folding variants to maintain their conformation and to form novel, biologically active complexes. We have identified unsaturated C18 fatty acids in the cis...

Abstract The Sac10b family consists of a group of highly conserved DNA binding proteins from both the euryarchaeotal and the crenarchaeotal branches of Archaea. The proteins have been suggested to play an architectural role in the chromosomal organization in these organisms. Previous studies have mainly focused on the Sac10b proteins from the crenarchaeota. Here, we report the 2.0 Å resolution crystal structure of Mja10b from the...

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