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Journal Issue - Volume 1 Issue 2 (February 1992)

Abstract The main goal of the protein evolutionist is the reconstruction of past events leading to the structures of contemporary proteins. The common strategy is to align amino acid sequences and make inferences about matters of common ancestry. The rate of change of amino acid sequence varies greatly from protein to protein, and this naturally affects how far back a given protein's ancestry can be traced. Happily, the rate of...

Abstract We develop a model for the reversible denaturation of proteins and for the effects of single‐site mutations on the denatured states. The model is based on short chains of sequences of H (hydrophobic) and P (other) monomers configured as self‐avoiding walks on the two‐dimensional square lattice. The N (native) state is defined as the unique conformation of lowest contact energy, whereas the D (denatured) state is defined as...

Abstract The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the...

Abstract A solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived from empirical vapor‐to‐water free energies of transfer of amino acid side‐chain analogs. The energy function and its derivatives were added to the CHARMM molecular simulation program (Brooks, B.R., Bruccoleri, R.E., Olafson,...

Abstract Calmodulin is a member of the “EF‐hand” family of Ca2+‐binding proteins. It consists of two homologous globular domains, each containing two helix‐loop‐helix Ca2+‐binding sites. To examine the contribution of individual Ca2+‐binding sites to the Ca2+‐binding properties of CaM, a series of four site‐directed mutants has been studied. In each, the glutamic acid at position 12 in one of the four Ca2+‐binding loops has been changed to a glutamine....

Abstract The kinetics of the reverse reaction catalyzed by Escherichia coli phosphofructokinase, i.e., the synthesis of ATP and fructose‐6‐phosphate from ADP and fructose‐1,6‐bisphosphate, have been studied at different pH values, from pH 6 to pH 9.2. Hyperbolic saturations of the enzyme are observed for both substrates. The affinity for fructose‐1,6‐bisphosphate decreases with pH following the ionization of a group with a pK of 6.6, whereas ...

Abstract Δ5‐3‐Ketosteroid isomerase (KSI: EC 5.3.3.1) of Pseudomonas testosteroni catalyzes the isomerization of Δ5‐3‐ketosteroids to Δ4‐3‐ketosteroids by the stereospecific transfer of the steroid 4β‐proton to the 6β‐position, using Tyr‐14 as a general acid and Asp‐38 as a base. Ultraviolet resonance Raman (UVRR) spectra have been obtained for the catalytically active double mutant Y55F + Y88F, which retains Tyr‐14 as the only tyrosine residue...

Abstract The terminal step of the heme biosynthetic pathway is catalyzed by the enzyme ferrochelatase (EC 4.99.1.1). In eukaryotes this enzyme is bound to the inner mitochondrial membrane with its active site facing the matrix side of the membrane. Previously this laboratory has characterized this enzyme via kinetic and protein chemical modification techniques, and with the recent cloning of the enzyme from yeast, mouse, and human...

Abstract The amino acid sequence of a protease inhibitor isolated from the hemolymph of Sarcophaga bullata larvae was determined by tandem mass spectrometry. Homology considerations with respect to other protease inhibitors with known primary structures assisted in the choice of the procedure followed in the sequence determination and in the alignment of the various peptides obtained from specific chemical cleavage at cysteines and enzyme...

Abstract The most abundant protein found in blood plasma from the sea lamprey (Petromyzon marinus) has the hallmarks of a plasma albumin: namely, high abundance, solubility in distilled water, a small number of tryptophans, and a high content of cysteines and charged residues. As in other vertebrate albumins, not all the cysteines are disulfide bonded. An unusual feature of this protein is its molecular weight of 175,000, roughly 2.5 times the...