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Journal Issue - Volume 4 Issue 2 (February 1995)

Abstract Ecotin, an Escherichia coli periplasmic protein of 142 amino acids, has been shown to be a potent inhibitor of a group of homologous serine proteases with widely differing substrate recognition. It is highly effective against a number of enzymes, including both pancreatic and neutrophil‐derived elastases, chymotrypsin, trypsin, factor Xa, and kallikrein. Recent structural and functional studies on ecotin and its...

Abstract The interplay between simulations at various levels of hydration and experimental observables has led to a picture of the role of solvent in thermodynamics and dynamics of protein systems. One of the most studied protein‐solvent systems is myoglobin, which serves as a paradigm for the development of structure‐function relationships in many biophysical studies. We review here some aspects of the solvation of myoglobin and...

  • Rearranging the domains of pepsinogen

  • Xinli Lin, Gerald Koelsch, Jeffrey A. Loy, Jordan Tang
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560040203 (p 159-166)

Abstract Most eukaryotic aspartic protease zymogens are synthesized as a single polypeptide chain that contains two distinct homologous lobes and a pro peptide, which is removed upon activation. In pepsinogen, the pro peptide precedes the N‐terminal lobe (designated pep) and the C‐terminal lobe (designated sin). Based on the three‐dimensional structure of pepsinogen, we have designed a pepsinogen polypeptide with the internal rearrangement of...

Abstract The kinetic folding mechanism for Escherichia coli dihydrofolate reductase postulates two distinct types of transient intermediates. The first forms within 5 ms and has substantial secondary structure but little stability. The second is a set of four species that appear over the course of several hundred milliseconds and have secondary structure, specific tertiary structure, and significant stability (Jennings PA, Finn BE, Jones ...

Abstract Tick anticoagulant peptide (TAP) is a potent and selective 60‐amino acid inhibitor of the serine protease Factor Xa (fXa), the penultimate enzyme in the blood coagulation cascade. The structural features of TAP responsible for its remarkable specificity for fXa are unknown, but the binding to its target appears to be unique. The elucidation of the TAP structure may facilitate our understanding of this new mode of serine...

Abstract The crystal structure of the gene V protein (GVP) from the Ff filamentous phages (M13, f1, fd) has been solved for the wild‐type and two mutant (Y41F and Y41H) proteins at high resolution. The Y41H mutant crystal structure revealed crystal packing interactions, which suggested a plausible scheme for constructing the polymeric protein shell of the GVP‐single‐stranded DNA (ssDNA) complex (Guan Y, et al., 1994, Biochemistry...

Abstract A cluster of highly conserved leucine side chains from residues 9, 68, 85, 94, and 98 is located in the hydrophobic heme pocket of cytochrome c. The contributions of two of these, Leu 85 and Leu 94, have been studied using a protein structure‐function‐mutagenesis approach to probe their roles in the maintenance of overall structural integrity and electron transfer activity. Structural studies of the L85C, L85F, L85M, and...

Abstract The covalent structure of umecyanin has been determined by a combination of classical Edman degradation sequence analysis and plasma desorption, laser desorption, and electrospray ionization mass spectrometry. The preparation appeared to contain two isoforms having either a valine (75%) or an isoleucine (25%) residue at position 48. The polypeptide chain of 115 amino acids is strongly heterogeneous at its C‐terminal end as...

Abstract Enolase (2‐phospho‐D‐glycerate hydrolase; EC 4.2.1.11) from the hyperthermophilic bacterium Thermotoga maritima was purified to homogeneity. The N‐terminal 25 amino acids of the enzyme reveal a high degree of similarity to enolases from other sources. As shown by sedimentation analysis and gel‐permeation chromatography, the enzyme is a 345‐kDa homooctamer with a subunit molecular mass of 48 ± 5 kDa. Electron microscopy and image...

Abstract The destabilizing effect of electrostatic repulsions on protein stability has been studied by using synthetic two‐stranded α‐helical coiled‐coils as a model system. The native coiled‐coil consists of two identical 35‐residue polypeptide chains with a heptad repeat QgVaGbAcLdQeKf and a Cys residue at position 2 to allow formation of an interchain disulfide bridge. This peptide, designed to contain no intrahelical or...

Abstract A new approach for investigating mechano‐chemical interactions in enzymes is described. The catalytic activity of crystalline crosslinked enzymes subjected to uniaxial deformation has been measured. Extension of monoclinic P21 crystals of carboxypeptidase A along the [010] direction leads to a many‐fold increase in catalytic esterase activity with no changes in the effective Michaelis constant. This increase is interpreted as due to...

Abstract Aspartate transcarbamoylase from Escherichia coli is a dodecameric enzyme consisting of two trimeric catalytic subunits and three dimeric regulatory subunits. Asp‐100, from one catalytic chain, is involved in stabilizing the C1‐C2 interface by means of its interaction with Arg‐65 from an adjacent catalytic chain. Replacement of Asp‐100 by Ala has been shown previously to result in increases in the maximal specific activity, ...

Abstract Study of the most conserved region in many β/α‐barrels, the phosphate‐binding site, revealed a sequence motif in a few β/α‐barrels with known tertiary structure, namely glycolate oxidase (GOX), cytochrome b2 (Cyb2), tryptophan synthase α subunit (TrpA), and the indoleglycerolphosphate synthase (TrpC). Database searches identified this motif in numerous other enzyme families: (1) IMP dehydrogenase (IMPDH) and GMP reductase (GuaC); (2)...

Abstract A pair of neural network‐based algorithms is presented for predicting the tertiary structural class and the secondary structure of proteins. Each algorithm realizes improvements in accuracy based on information provided by the other. Structural class prediction of proteins nonhomologous to any in the training set is improved significantly, from 62.3% to 73.9%, and secondary structure prediction accuracy improves slightly,...

Abstract The de novo design of αtα, a helical hairpin peptide, is described. αtα (α‐helix/turn/α‐helix) was developed to provide a model system for protein folding at the level of secondary structure association and stabilization. According to the prevailing models of protein folding, the second step in the folding process is the association and stabilization of secondary structural elements or microdomains. A brief description of...

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