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Journal Issue - Volume 3 Issue 4 (April 1994)

Abstract We propose that arginine side chains often play a previously unappreciated general structural role in the maintenance of tertiary structure in proteins, wherein the positively charged guanidinium group forms multiple hydrogen bonds to backbone carbonyl oxygens. Using as a criterion for a “structural” arginine one that forms 4 or more hydrogen bonds to 3 or more backbone carbonyl oxygens, we have used molecular graphics to locate...

Abstract We examine the role of the conformational restriction imposed by constrained ends of a protein loop on the determination of a strained loop conformation. The Lys 116‐Pro 117 peptide bond of staphylococcal nuclease A exists in equilibrium between the cis and trans isomers. The folded protein favors the strained cis isomer with an occupancy of 90%. This peptide bond is contained in a solvent‐exposed, flexible loop of residues 112‐117...

Abstract Neural networks were used to generalize common themes found in transmembrane‐spanning protein helices. Various‐sized databases were used containing nonoverlapping sequences, each 25 amino acids long. Training consisted of sorting these sequences into 1 of 2 groups: transmembrane helical peptides or nontransmembrane peptides. Learning was measured using a test set 10% the size of the training set. As training set size...

Abstract One of the major goals of molecular biology is to understand how protein chains fold into a unique 3‐dimensional structure. Given this knowledge, perhaps the most exciting prospect will be the possibility of designing new proteins to perform designated tasks, an application that could prove to be of great importance in medicine and biotechnology. It is possible that effective protein design may be achieved without the...

Abstract Bio‐Rex 70 chromatography was combined with reverse‐phase (RP) HPLC to fractionate histone H1° and 4 histone H1 subtypes from human placental nuclei as previously described (Parseghian MH et al., 1993, Chromosome Res 1:127‐139). After proteolytic digestion of the subtypes with Staphylococcus aureus V8 protease, peptides were fractionated by RP‐HPLC and partially sequenced by Edman degradation in order to correlate them with human...

Abstract Three‐dimensional structural analysis of physiologically important serine proteases is useful in identifying functional features relevant to the expression of their activities and specificities. The human serine protease anticoagulant protein C is currently the object of many genetic site‐directed mutagenesis studies. Analyzing relationships between its structure and function and between naturally occurring mutations and...

Abstract Isoprenyl diphosphate synthases are ubiquitous enzymes that catalyze the basic chain‐elongation reaction in the isoprene biosynthetic pathway. Pairwise sequence comparisons were made for 6 farnesyl diphosphate synthases, 6 geranylgeranyl diphosphate synthases, and a hexaprenyl diphosphate synthase. Five regions with highly conserved residues, two of which contain aspartate‐rich DDXX(XX)D motifs found in many...

Abstract The DNA binding domain of the GAL4 transcription factor from yeast is located in the N‐terminal 60 residues of the polypeptide of 881 amino acids. This domain binds 2 Zn ions, which form a binuclear cluster, Zn2C6 with 6 C residues, two of which bridge the 2 metal ions (Gardner KH et al., 1991, Biochemistry 30:11292‐11302). Binding of Zn or Cd to GAL4 induces the conformation of the protein necessary to recognize the specific DNA ...

Abstract The serine proteinase inhibitor antithrombin III (ATIII) is a key regulatory protein of intrinsic blood coagulation. ATIII attains its full biological activity only upon binding polysulfated oligosaccharides, such as heparin. A series of synthetic peptides have been prepared based on the proposed heparin binding regions of ATIII and their ability to bind heparin has been assessed by CD spectrometry, by isothermal titration...

Abstract We used frequency‐domain measurements of fluorescence resonance energy transfer to measure the distribution of distances between Trp‐19 of melittin and a 1‐dimethylamino‐5‐sulfonylnaphthalene (dansyl) residue on the N‐terminal‐α‐amino group. Distance distributions were obtained for melittin free in solution and when complexed with calmodulin (CaM), troponin C (TnC), or palmitoyloleoyl‐L‐α‐phosphatidylcholine (POPC)...

Abstract The slow refolding of guanidine‐HC1‐denatured ribonuclease‐A was studied by volume change and by kinetic CD at 222 and 276 nm. Dilatometric measurements revealed that on refolding there is a fast volume change of +232 mL/mol of protein. This is followed by a very slow nonexponential change that takes about 25 min to reach equilibrium. By adding varying amounts of (NH4)2SO4, the slow volume change curve was resolved into 2 concurrent...

Abstract The diffusion‐collision model of protein folding is assessed. A description is given of the qualitative aspects and quantitative results of the diffusion‐collision model and their relation to available experimental data. We consider alternative mechanisms for folding and point out their relationship to the diffusion‐collision model. We show that the diffusion‐collision model is supported by a growing body of experimental...

  • Thermodynamics of barnase unfolding

  • Yuri V. Griko, George I. Makhatadze, Peter L. Privalov, Robert W. Hartley
  • Published in Wiley Interscience on Dec 24, 2008
  • DOI: 10.1002/pro.5560030414 (p 669-676)

Abstract The thermodynamics of barnase denaturation has been studied calorimetrically over a broad range of temperature and pH. It is shown that in acidic solutions the heat denaturation of barnase is well approximated by a 2‐state transition. The heat denaturation of barnase proceeds with a significant increase of heat capacity, which determines the temperature dependencies of the enthalpy and entropy of its denaturation. The...

Abstract A technique is described for the rapid, sensitive analysis of posttranslational modifications of proteins that have been separated by 2‐dimensional electrophoresis and blotted onto a membrane with a cationic surface. The isolated protein spots visualized by reverse staining of the blotting membrane are excised, washed, and subjected to chemical (cyanogen bromide) and/or enzymatic (endoproteinase Lys‐C) degradation directly...

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