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Journal Issue - Volume 15 Issue 10 (October 2006)

Abstract Origami is the Japanese art of folding a piece of paper into complex shapes and forms. Much like origami of paper, Nature has used conserved protein folds to engineer proteins for a particular task. An example of a protein family, which has been used by Nature numerous times, is the thioredoxin superfamily. Proteins in the thioredoxin superfamily are all structured with a β‐sheet core surrounded with α‐helices, and most...

Abstract We describe an alternate approach for studying protein structure using the detection of ultraviolet (UV) absorbance peak shifts of aromatic amino acid side chains induced by the presence of salts. The method is based on the hypothesis that salt cations (Li+, Na+, and Cs+) of varying sizes can differentially diffuse through protein matrices and interact with benzyl, phenyl, and indole groups through cation–π interactions. We...

Abstract Lymphocyte Antigen 6 (Ly‐6) superfamily members are cysteine‐rich, generally GPI‐anchored cell surface proteins, which have definite or putative immune related roles. There are 27 members of this family described so far in the human genome and 37 in the mouse. Five of them are clustered in the class III region of the human and mouse MHCs. Following computational analyses, we functionally characterized the encoded proteins...

Abstract φ‐Values provide an important benchmark for the comparison of experimental protein folding studies to computer simulations and theories of the folding process. Despite the growing importance of φ measurements, however, formulas to quantify the precision with which φ is measured have seen little significant discussion. Moreover, a commonly employed method for the determination of standard errors on φ estimates assumes...

Abstract Here, we propose a binding site prediction method based on the high frequency end of the spectrum in the native state of the protein structural dynamics. The spectrum is obtained using an elastic network model (GNM). High frequency vibrating (HFV) residues are determined from the fastest modes dynamics. HFV residue clusters and the associated surface patch residues are tested for their likelihood to locate at the binding...

Abstract A good approach to test our current knowledge on formation of protein β‐sheets is de novo protein design. To obtain a three‐stranded β‐sheet mini‐protein, we have built a series of chimeric peptides by taking as a template a previously designed β‐sheet peptide, Betanova‐LLM, and incorporating N‐ and/or C‐terminal extensions taken from WW domains, the smallest natural β‐sheet domain that is stable in absence of disulfide...

Abstract A computational model was developed to examine the phototriggered folding of a caged protein, a protein modified with an organic photolabile cross‐linker. Molecular dynamics simulations of the modified 36‐residue fragment of subdomain B of chicken villin head piece with a photolabile linker were performed, starting from both the caged and the uncaged structures. Construction of a free‐energy landscape, based on principal components as well as on...

Abstract A large fraction of the Mycobacterium tuberculosis genome codes for proteins of unknown function. We here report the structure of one of these proteins, Rv0130, solved to a resolution of 1.8 å. The Rv0130 monomer features a single hotdog fold composed of a highly curved β‐sheet on top of a long and a short α‐helix. Two monomers in turn pack to form a double‐hotdog‐folded homodimer, similar to a large group of enzymes that...

Abstract As part of a functional analysis of archaeal Sm‐related proteins, we have studied the oligomerization behavior of the Sm‐2 type protein from the euryarchaeon Archaeoglobus fulgidus using gel filtration chromatography and noncovalent mass spectrometry. Our experiments show that the oligomeric state of the protein depends on the pH and presence of RNA. The protein forms a hexamer at acidic pH in the absence of RNA. The addition ...

Abstract The extracellular part of the fibroblast growth factor (FGF) receptor (FGFR) consists of up to three Ig modules (Ig1–Ig3), in which the Ig2 and Ig3 modules determine affinity and specificity for FGF and heparin. The FGFR isoforms lacking the Ig1 module have higher affinity for FGF and heparin than the triple Ig‐module isoforms, suggesting that the Ig1 module is involved in the regulation of the FGFR–ligand interaction. We...

Abstract Engineering of alternative binding sites on the surface of an enzyme while preserving the enzymatic activity would offer new opportunities for controlling the activity by binding of non‐natural ligands. Loops and turns are the natural substructures in which binding sites might be engineered with this purpose. We have genetically inserted random peptide sequences into three relatively rigid and contiguous loops of the TEM‐1...

Abstract Libraries of phage‐displayed β‐lactamase mutants in which up to three loops have been engineered by genetic introduction of random peptide sequences or by randomization of the wild‐type sequence have been submitted to selection protocols designed to find mutants in which binding of transition metal ions to the engineered secondary binding site leads to significant effects on the enzymatic activity. A double‐selection...

Abstract The interaction of cellular proteins with the gap junction protein Connexin43 (Cx43) is thought to form a dynamic scaffolding complex that functions as a platform for the assembly of signaling, structural, and cytoskeletal proteins. A high stringency Scansite search of rat Cx43 identified the motif containing Ser373 (S373) as a 14‐3‐3 binding site. The S373 motif and the second best mode‐1 motif, containing Ser244 (S244),...

Abstract Exploitation of potential new targets for drug and vaccine development has an absolute requirement for multimilligram quantities of soluble protein. While recombinant expression of full‐length proteins is frequently problematic, high‐yield soluble expression of functional subconstructs is an effective alternative, so long as appropriate termini can be identified. Bioinformatics localizes domains, but doesn't predict...

Abstract The rise in the number of functionally uncharacterized protein structures is increasing the demand for structure‐based methods for functional annotation. Here, we describe a method for predicting the location of a binding site of a given type on a target protein structure. The method begins by constructing a scoring function, followed by a Monte Carlo optimization, to find a good scoring patch on the protein surface....

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