摘要:

AbstractIn our previous paper we reported the conformation of melittin bound to perdeuterated dodecylphosphocholine micelles as studied by1H NMR experiment and distance geometry calculation. No hydrogen bonds were taken into consideration explicitly in the calculation. However, mostly α‐helical conformations were obtained as results of the calculation even with no explicitly assumed hydrogen bonds. In the present paper we refined the distance geometry calculation by incorporating hydrogen bonds suggested by the previous calculation. As a result, we obtained the conformation of melittin, which was consistent with both NMR data and the additional hydrogen bonding data. The α‐helical rod in the refined conformation also has a kink at Thr‐11 and Gly‐12, but its bent angle is now a bit narrowly distributed in 135° × 15°. In the present study another distortion at Trp‐19 and IIe‐20 becomes conspicuous. The average root‐mean‐square displacement of atoms is now much smaller and is 1.5 Å for all backbone atoms. In the present paper side chain conformati

ISSN:0887-3585    

DOI:10.1002/prot.340090202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractTo study the role of Pro residues in the conformation and conformational stability of a protein, nine mutant α subunits of tryptophan synthase fromEscherichia coli, in which Ala or Gly was substituted for each of six Pro residues (positions 28, 57, 62, 96, 132, and 207) that are conserved in 10 microoganisms, were constructed by means of site‐directed mutagenesis. The far‐ultraviolet (UV) CD spectra of five mutant α subunits with Ala in place of Pro were identical to the spectrum of the wild‐type protein, the exception being the mutant at position 207 (P207A). CD values in the far‐UV region were less negative for P207A, indicating that the Pro residue at position 207 plays a role in maintaining the intact structure of the α subunit. The negative CD values of the Gly mutants examined (P28G, P96G, and P132G) were also decreased. Calorimetric measurements showed that the two mutants at position 28 (P28G and P28A) gave two peaks in the excess heat capacity curve, whereas the wild type and other Pro mutants had only a single peak. The stability of each mutant protein relative to that of the wild type was about the same for P57A, less for P62A and P132A, and markedly decreased for P96A and P207A, which are substituted at less mobile positions. The changes of denaturation entropy (ΔΔdS) at the denaturation temperature of the wild‐type protein (54.1 °C at pH 9.0) were positive for P57A, P62A, and P132A, but negative for P96A, P207A, and P132G. The present results do not indicate that the differences in stability (ΔdG) among Pro substitutions are caused only by an entropic factor, as might be theoretically expected. The decreases in stability for P96A and P207 were due to the considerable decrease in denaturation enthalpy, although they were partly compensated for by the decrease in entropy. Our results also suggest that Pro‐28 stabilizes the interaction between two domain

ISSN:0887-3585    

DOI:10.1002/prot.340090203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractIntrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high‐resolution protein structures in order to evaluate the prevalence and geometry of sulfur‐containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians intersted in protein structure and protein engineer

ISSN:0887-3585    

DOI:10.1002/prot.340090204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractA statistical analysis of ion pairs in protein crystal structures shows that their abundance with respect to uncharged controls is accurately predicted by a Botlzmann‐like function of electrostatic potential. It appears that the mechanisms of protein folding and/or evolution combine to produce a “thermal” distribution of local nonbonded interactions, as has been suggested by statistical–mechanical theories. Using this relationship, we develop a maximum likelihood methodology for estimation of apparent energetic parameters from the data base of known structures, and we derive electrostatic potential functions that lead to optimal agreement of observed and predicted ion‐pair frequencies. These are similar to potentials of mean force derived from electrostatic theory, but departure from Coulombic behavior is less than has been

ISSN:0887-3585    

DOI:10.1002/prot.340090205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractThe DNA and protein sequences of single‐stranded DNA binding proteins (SSBs) encoded by the plP71a, plP231a, and R64 conjugative plasmids have been determined and compared toEscherichia coliSSB and the SSB encoded by F‐plasmid. Although the amino acid sequences of all of these proteins are highly conserved within the NH2‐terminal two‐thirds of the protein, they diverge in the COOH‐terminal third region. A number of amino acid residues which have previously been implicated as being either directly or indirectly involved in DNA binding are conserved in all of these SSBs. These residues include Trp‐40, Trp‐54, Trp‐88, His‐55, and Phe‐60. On the basis of these sequence comparisons and DNA binding studies, a role for Tyr‐70 in DNA binding is suggested for the first time. Although the COOH‐terminal third of these proteins diverges more than their NH2‐terminal regions, the COOH‐terminal five amino acid residues of all five of these proteins are identical. In addition, all of these proteins share the characteristic property of having a protease resistant, NH2‐terminal core and an acidic COOH‐terminal region. Despite the high degree of sequence homology among the plasmid SSB proteins, the F‐plasmid SSB appears unique in that it was the only SSB tested that neither bound well to poly(dA) nor was able to stimulate DNA polymerase III holoenzyme elongation rates. Poly [d(A‐T)] melting studies suggest that at least three of the plasmid encoded SSBs are better helix‐destabilizing p

ISSN:0887-3585    

DOI:10.1002/prot.340090206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractUridine diphosphogalactose‐4‐epimerase fromE. colihas been crystallized in a form suitable for a high‐resolution X‐ray crystallographic structural analysis. The enzyme complexed with a substrate analogue, uridine diphosphobenzene (UDP‐benzene), crystallizes readily using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space groupP212121with unit cell dimensions,a= 76.3 Å,b= 83.1 Å, andc= 132.1 Å. Based on still setting photographs, the crystals diffract to a nominal resolution of 2.3 Å and are stable in the X‐ray beam. The enzyme used in these experiments was produced by a new expression system and a modified puri

ISSN:0887-3585    

DOI:10.1002/prot.340090207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractUsing an incomplete factorial experimental design, we have identified conditions for crystallization of yeast orotidine 5′‐monophosphate decarboxylase (ODCase) in an unliganded state and complexed separately to two inhibitors: 6‐azauridine 5′‐monophosphate (aza‐UMP) and 1‐(5′‐phospho‐β‐D‐ribofuranosyl) barbituric acid (BMP). Crystals of X‐ray diffraction quality have been obtained of yeast ODCase complexed with BMP, a putative transition state analog inhibitor (Ki= 8.8 × 10−12M). ODCase:BMP complex crystals with a hexagonal rod habit were grown from a solution initially containing 12 mg/ml ODCase (205 μM dimer) plus 450 μM BMP by microdialysis at 4°C against a mother liquor which consisted of 0.1 M Na‐PIPES‐acetate (pH 6.4), 37.5 μM BMP, 5 mM mercaptoethanol, 1% polyethylene glycol 400, and 2.3 M ammonium sulfate. Crystals were analyzed using precession photography and were assigned to trigonal space groupR32 with unit cell dimensionsa=b= 115 Å,c= 385 Å. The crystal density is 1.245 g/cm3indicating the presence of two ODCase:BMP complex dimers (118 kDa each) per asymmetric unit with a packing density of 2.08 Å3/Da and 41% solvent content. The morphological habit of crystals of the ODCase:BMP complex changed when the initial ammonium sulfate concentration was increased in 0.05 M steps from 2.3 to 2.45 M. All of these crystals diffracted to at least 3.0 Å resolution over a period of several week

ISSN:0887-3585    

DOI:10.1002/prot.340090208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340090201

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY