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Journal Issue - Volume 4 Issue 7 (July 1995)

Abstract The astacin family of metalloendopeptidases was recognized as a novel family of proteases in the 1990s. The crayfish enzyme astacin was the first characterized and is one of the smallest members of the family. More than 20 members of the family have now been identified. They have been detected in species ranging from hydra to humans, in mature and in developmental systems. Proposed functions of these proteases include...

Abstract The structure of adenylate kinase from yeast ligated with the two‐substrate‐mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 Å resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 Å. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G‐proteins shows that Mg2+ is exactly...

Abstract Hemoglobin (Hb) S containing Leu, Ala, Thr, or Trp substitutions at β85 were made and expressed in yeast in an effort to evaluate the role of Phe‐β85 in the acceptor pocket during polymerization of deoxy Hb S. The four Hb S variants have the same electrophoretic mobility as Hb S, and these β385 substitutions do not significantly affect heme‐globin interactions and tetramer helix content. Hb S containing Trp‐β85 had...

Abstract The solution secondary structure of calcium‐saturated skeletal troponin C (TnC) in the presence of 15% (v/v) trifluoroethanol (TFE), which has been shown to exist predominantly as a monomer (Slupsky CM, Kay CM, Reinach FC, Smillie LB, Sykes BD, 1995, Biochemistry 34, forthcoming), has been investigated using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The 1H, 15N, and 13C NMR chemical shift values for TnC in...

Abstract We used sequence and structural comparisons to determine the fold for eukaryotic ornithine decarboxylase, which we found is related to alanine racemase. These enzymes have no detectable sequence identity with any protein of known structure, including three pyridoxal phosphate‐utilizing enzymes. Our studies suggest that the N‐terminal domain of ornithine decarboxylase folds into a β/α‐barrel. Through the analysis of known...

Abstract The thermodynamic basis of helix stability in peptides and proteins is a topic of considerable interest. Accordingly, we have computed the interactions between side chains of all hydrophobic residue pairs and selected triples in a model helix, using Boltzmann‐weighted exhaustive modeling. Specifically, all possible pairs from the set Ala, Cys, His, Ile, Leu, Met, Phe, Trp, Tyr, and Val were modeled at spacings of (i, i +...

Abstract The heat capacity, enthalpy, entropy, and Gibbs energy changes for the temperature‐induced unfolding of 11 globular proteins of known three‐dimensional structure have been obtained by microcalorimetric measurements. Their experimental values are compared to those we calculate from the change in solvent‐accessible surface area between the native proteins and the extended polypeptide chain. We use proportionality coefficients...

Abstract We have determined the N‐ and C‐capping preferences of all 20 amino acids by substituting residue X in the peptides NH2‐XAKAAAAKAAAAKAAGY‐CONH2 and in Ac‐YGAAKAAAAKAAAAKAX‐CO2H. Helix contents were measured by CD spectroscopy to obtain rank orders of capping preferences. The data were further analyzed by our modified Lifson‐Roig helix‐coil theory, which includes capping parameters (n and c), to find free energies of capping (‐RT In n and —RT In...

Abstract Avidin is a tetramer of 16‐kDa subunits that have a high affinity for biotin. Proteolysis of native apoavidin by proteinase K results in a limited attack at the loop between β‐strands 3 and 4, involving amino acids 38–43. Specifically, sites of proteolysis are at Thr 40‐Ser 41 and Asn 42‐Glu 43. The limited proteolysis results in an avidin product that remains otherwise intact and which has enhanced binding for...

Abstract Mathematical modeling was used to evaluate experimental data for bacterial binding protein‐dependent transport systems. Two simple models were considered in which ligand‐free periplasmic binding protein interacts with the membrane‐bound components of transport. In one, this interaction was viewed as a competition with the ligand‐bound binding protein, whereas in the other, it was considered to be a consequence of the...

Abstract We have developed a simple approach for the evaluation of the free energies of inhibitor binding to the protease of the human immunodeficiency virus (HIV‐1 PR). Our algorithm is based on the observation that most groups that line the binding pockets of this enzyme are hydrophobic in nature. Based on this fact, we have likened the binding of an inhibitor to this enzyme to its transfer from water to a medium of lower...

Abstract The specificity of GalNAc‐transferase is consistent with the existence of an extended site composed of nine sub‐sites, denoted by R4, R3, R2, Rb R0, R1, R2′, R3′, and R4, where the acceptor at R0 is either Ser or Thr to which the reducing monosaccharide is being anchored. To predict whether a peptide will react with the enzyme to form a Ser‐ or Thr‐conjugated glycopeptide, a new method has been proposed based on the vector‐projection...

Abstract This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X‐ray‐determined fractional components (FC) of secondary structure. Predictive capability...

Abstract A new model for calculating the solvation energy of proteins is developed and tested for its ability to identify the native conformation as the global energy minimum among a group of thousands of computationally generated compact non‐native conformations for a series of globular proteins. In the model (called the WZS model), solvation preferences for a set of 17 chemically derived molecular fragments of the 20 amino acids...

Abstract We present an automated method for modeling backbones of protein loops. The method samples a database of ϕi+1 and Ψi angles constructed from a nonredundant version of the Protein Data Bank (PDB). The dihedral angles ϕi+1 and Ψi completely define the backbone conformation of a dimer when standard bond lengths, bond angles, and a trans planar peptide configuration are used. For the 400 possible dimers resulting from 20 natural amino acids, a list of allowed ...

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