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Journal Issue - Volume 12 Issue 6 (June 2003)

Abstract The conformational equilibrium between 310‐ and α‐helical structure has been studied via high‐resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac‐AMAAKAWAAKA AAARA‐NH2. Their 750‐MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 310‐helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous...

Abstract We address the problem of clustering the whole protein content of genomes into three different categories—globular, all‐α, and all‐β membrane proteins—with the aim of fishing new membrane proteins in the pool of nonannotated proteins (twilight zone). The focus is then mainly on outer membrane proteins. This is performed by using an integrated suite of programs (Hunter) specifically developed for predicting the occurrence of...

Abstract It was established previously that helical propensities of different amino acid residues in the middle of α‐helix in peptides and in proteins are very similar. The statistical analysis of the protein helices from the known three‐dimensional structures shows no difference in the frequency of noncharged residues in the middle and at the C terminus. Yet, experimental studies show distinctive differences for the helical...

Abstract Understanding, and ultimately predicting, how a 1‐D protein chain reaches its native 3‐D fold has been one of the most challenging problems during the last few decades. Data increasingly indicate that protein folding is a hierarchical process. Hence, the question arises as to whether we can use the hierarchical concept to reduce the practically intractable computational times. For such a scheme to work, the first step is to...

Abstract The well‐known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N‐formyl group (Hi−1−C′i−1=Oi−1), in which Hi−1 presents less steric hindrance than does Oi−1, likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n → π* interaction between the oxygen of the...

Abstract β‐1,4‐Galactanases hydrolyze the galactan side chains that are part of the complex carbohydrate structure of the pectin. They are assigned to family 53 of the glycoside hydrolases and display significant variations in their pH and temperature optimum and stability. Two fungal β‐1,4‐galactanases from Myceliophthora thermophila and Humicola insolens have been cloned and heterologously expressed, and the crystal structures of the gene...

Abstract The GrpE heat shock protein from Escherichia coli has a homodimeric structure. The dimer interface encompasses two long α‐helices at the NH2‐terminal end from each monomer (forming a “tail”), which lead into a small four‐helix bundle from which each monomer contributes two short sequential α‐helices in an antiparallel topological arrangement. We have created a number of different deletion mutants of GrpE that have portions of the dimer...

Abstract For high‐throughput protein structural analysis, it is indispensable to develop a reliable protein overexpression system. Although many protein overexpression systems, such as that involving Escherichia coli cells, have been developed, the number of overexpressed proteins showing the same biological activities as those of the native proteins is limited. A novel wheat germ cell‐free protein synthesis system was developed recently, and...

Abstract Transthyretin (TTR) is one of the known human amyloidogenic proteins. Its native state is a homotetramer with each monomer having a β‐sandwich structure. Strong experimental evidence suggests that TTR dissociates into monomeric intermediates and that the monomers subsequently self‐assemble to form amyloid deposits and insoluble fibrils. However, details on the early steps along the pathway of TTR amyloid formation are...

Abstract Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium‐accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium‐accuracy protein backbone structures. Our strategy...

Abstract In most cases aminoacyl‐tRNA synthetases (aaRSs) are negatively charged, as are the tRNA substrates. It is apparent that there are driving forces that provide a long‐range attraction between like charge aaRS and tRNA, and ensure formation of “close encounters.” Based on numerical solutions to the nonlinear Poisson‐Boltzmann equation, we evaluated the electrostatic potential generated by different aaRSs. The 3D‐isopotential...

Abstract Osmolytes increase the thermodynamic conformational stability of proteins, shifting the equilibrium between native and denatured states to favor the native state. However, their effects on conformational equilibria within native‐state ensembles of proteins remain controversial. We investigated the effects of sucrose, a model osmolyte, on conformational equilibria and fluctuations within the native‐state ensembles of bovine...

Abstract Structural perturbation of α‐crystallin is shown to enhance its molecular chaperone‐like activity in preventing aggregation of target proteins. We demonstrate that arginine, a biologically compatible molecule that is known to bind to the peptide backbone and negatively charged side‐chains, increases the chaperone‐like activity of calf eye lens α‐crystallin as well as recombinant human αA‐ and αB‐crystallins....

Abstract A protein–protein docking approach has been developed based on a reduced protein representation with up to three pseudo atoms per amino acid residue. Docking is performed by energy minimization in rotational and translational degrees of freedom. The reduced protein representation allows an efficient search for docking minima on the protein surfaces within. During docking, an effective energy function between pseudo atoms...

Abstract FSD‐1 (full sequence design 1) is a protein folded in a ββα motif, designed on the basis of the second zinc finger domain of Zif268 by a substitution of its metal coordination site with a hydrophobic core. In this work, we analyzed the possibility of introducing the DNA recognition motif of the template zinc finger (S13RSDH17) into FSD‐1 sequence in order to obtain a small DNA‐binding module devoid of cross‐link(s) or metal cofactors....

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