ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEstimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximationSanzo Miyazawa and Robert L. JerniganCite this: Macromolecules 1985, 18, 3, 534–552Publication Date (Print):March 1, 1985Publication History Published online1 May 2002Published inissue 1 March 1985https://pubs.acs.org/doi/10.1021/ma00145a039https://doi.org/10.1021/ma00145a039research-articleACS PublicationsRequest reuse...

cDNA clones for rat acyl-CoA oxidase were isolated. The 3.8-kilobase mRNA sequence of the enzyme was completely covered by two overlapping clones. composite consisted 3741 bases and contained a 1983-base open reading frame which encodes polypeptide 661 amino acid residues. Two species identified. They differed in their coding nucleotide sequences, only within small region. same number nucleotides can be translated common frame. are 55% 50% homologous above region at levels, respectively....

Lotus tetragonolobus agglutinin (LTA) binds preferentially to early embryonic cells in the mouse. The affinity-purified antibody raised against LTA receptors from embryonal carcinoma were used screen a lambda gt11 expression library of F9 cells, resulting detection cDNA clone specifying new glycoprotein termed "basigin." has been suggested be transmembrane one, and was found member immunoglobulin (Ig) superfamily. molecular weight basigin largely range between 43,000 66,000, while that...

Abstract For the studies on mechanism of induction peroxisomal beta-oxidation enzymes and biogenesis organelle, we have isolated cDNA clones for rat enoyl-CoA: hydratase-3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme. On blotting experiments with liver RNA, cDNAs hybridized to a 3.0-kilobase RNA which was increased 5-7-fold by administration di-(2-ethylhexyl)phthalate rats. Nucleotide sequencing carried out four cloned one obtained primer extension method. By overlapping these sequences...

Pairwise contact energies for 20 types of residues are estimated self-consistently from the actual observed frequencies contacts with regression coefficients that obtained by comparing "input" and predicted values Bethe approximation equilibrium mixtures interacting. This is premised on fact correlations between sufficiently high although themselves can depend to some extent protein structures as well interaction strengths. Residue coordination numbers optimized obtain best correlation...

We have isolated five cDNA clones for rat liver catalase (hydrogen peroxide:hydrogen peroxide oxidoreductase, EC 1.11.1.6). These overlapped with each other and covered the entire length of mRNA, which had been estimated to be 2.4 kilobases long by blot hybridization analysis electrophoretically fractionated RNA. Nucleotide sequencing was carried out on these composite nucleotide sequence determined. The 5' noncoding region contained 83 bases followed 1581 an open reading frame that encoded...

In mice, 12 germ-line DH genes belonging to three different families (DQ52, DSP2 and DFL16) have been identified. The other than DQ52 are clustered in the 60 kb-long region located between VH JH genes. Since there seven gene (DHQ52, DXP, DA, DK, DN, DM DLR) humans, we tried identify new using human probes. Mouse showing highest similarity were mouse DFL16 DA Southern hybridization of clones covering 60-kb with probes did not detect any Nucleotide sequence analysis 4.0-kb fragment containing...

Three peroxisomal enzymes of &oxidation from rat liver were synthesized in a cell-free protein-synthesizing system derived lysate rabbit reticulocytes.The vitro products acyl-CoA oxidase (EC 1.3.99.3) and bifunctional protein containing enoyl-CoA hydratase 4.2.1.17)and 3-hydroxyacyl-CoA dehydrogenase 1.1.1.35)activities apparently the same size charge as subunit respective mature enzymes; that 3-ketoacyl-CoA thiolase 2.3.1.16)was about 3,000 Da larger more basic than its subunit.The free...

The minimal sequence requirement for a peroxisome-targeting signal was investigated using an in vitro import system. Carboxyl-terminal sequences Ser-Lys-Leu (SKL) and Leu-Gln-Ser-Lys-Leu (LQSKL) of acyl-CoA oxidase (AOX) directed to peroxisomes the fused proteins with import-incompetent forms AOX catalase that had been truncated, implying SKL tripeptide functions as targeting signal. Elimination entire or deletion any 1 2 amino acids abolished activity AOX. Substitution alanine serine did...

The amino-terminal presequences of rat peroxisomal 3-ketoacyl-CoA thiolase precursors (types A and B) were reported to be cleavable signal peptides for protein translocation. In the present study, this was proven by immunoelectron microscopy cultured Chinese hamster ovary cells stably expressing fusion proteins sequences precursor Escherichia coli dihydrofolate reductase. processed into mature forms apparently correct sizes. Site-directed mutagenesis studies charged residues in B-type...

We consider modifications of an empirical energy potential for fold and sequence recognition to represent approximately the stabilities proteins in various environments. A used here includes a secondary structure representing short-range interactions structures proteins, tertiary consisting long-range, pairwise contact repulsive packing potential. This is devised evaluate together total conformational protein at coarse grained residue level. It was previously estimated from observed...

Adipocyte-derived leucine aminopeptidase (A-LAP) is a recently identified novel member of the M1 family zinc-metallopeptidases. Transfection A-LAP cDNA into COS-7 cells resulted in secretion enzyme. In this study, recombinant was expressed Chinese hamster ovary cells, purified to homogeneity and its enzymatic properties were characterized. The enzyme active towards synthetic substrate, L-leucyl-p-nitroanilide, yielding V(max) 3.55 micromol/min/mg K(m) 1.28 mM, shown be monomeric protein with...

Overlapping genomic clones containing the entire sequence of rat acyl-CoA oxidase gene were isolated and characterized.This spans about 25 kilobases, there are 14 exons 13 introns.All exon-intron junction sequences agree with GT/ AG rule.The results Southern blot analyses indicated that occurs once per haploid genome.

A systematic study was carried out on mutability of amino acid residues in evolving proteins relation to their polarity and location within three‐dimensional structure proteins. Exteriority residue sites is quantitatively defined as accessibility based static accessible surface area solvent water molecule. Residue are classified into interior exterior depending accessibility. More frequent substitution confirmed be general eight sets homologous protein families regardless biological...

Probabilities of all possible correspondences residues in aligning two proteins are evaluated by assuming that the statistical weight each alignment is proportional to exponent its total similarity score. Based on such probabilities, a probability includes most probable proposed. In cases highly similar sequence pairs, alignments agree with maximum correspond Significant those whose probabilities >0.5. The method applied few protein and results indicate probably correct structural incorrect...

The instabilities of the native structures mutant proteins with an amino acid exchange are estimated by using contact energy and number contacts for each type pair, which were from 18,192 residue-residue observed in 42 crystals globular proteins. They then used to evaluate a transition probability matrix codon substitutions log relatedness odds matrix, is as scoring measure similarity between protein sequences. To consider homologous proteins, base mutation rates effects genetic code also...

The stability changes caused by single amino acid substitutions are studied a simple, empirical method which takes account of the free energy change in compact denatured state as well native state. conformational is estimated from effective inter-residue contact energies, evaluated our previous study. When this applied, with simple assumption about compactness state, for replacements at Glu49 tryptophan synthase alpha subunit and Ile3 bacteriophage T4 lysozyme, estimates unfolding Gibbs...

We estimate the statistical distribution of relative orientations between contacting residues from a database protein structures and evaluate potential mean force for residues. Polar angles Euler are used to specify two degrees directional freedom three rotational orientation one residue another in residues, respectively. A local coordinate system affixed each based only on main chain atoms is defined fold recognition. The number pairs will severely limit resolution orientations, if it...

The etiology of 3-ketothiolase deficiency has been attributed to a defect mitochondrial acetoacetyl-CoA thiolase because the activity in related materials is not activated by K+, property characteristic for this enzyme. We studied enzyme protein and biosynthesis thiolase, using cultured skin fibroblasts from 5-yr-old boy with deficiency. following results were obtained. (a) Activation K+ was nil; (b) affected treatment antibody against thiolase; (c) A signal detected immunoblot analysis; (d)...

A poled single crystal of LiNbO3 doped with Rh as a new impurity is described in terms its storage performance producing high-efficiency simple phase holograms. Doping introduces absorption band peaking around 4880 Å, and dramatically improves the recording sensitivity, diffraction efficiency, erasing persistence holograms over undoped crystal. Anomalous optical erasure, possibly due to self-enhancement hologram, also observed our

When D-3-hydroxyacyl-CoA dehydratase/D-3-hydroxyacyl-CoA dehydrogenase bifunctional protein was purified from human liver, two preparations were obtained. One contained a 77-kDa polypeptide as the main component and minor smaller polypeptides including 46-kDa polypeptide, this preparation showed both dehydratase activities. The other homodimer of only activity. Further analysis indicated that native enzyme is which proteolytically modified during purification. cDNA for cloned. amino acid...