摘要:

AbstractA systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins—20 out of a total of 49—belong to either one of two loop types previously described by Thornton and co‐workers. Six loops are of the αβ1 type, with one residue between the α‐helix and β‐strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β‐strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β‐strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α‐helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β‐sheet surface and of main chain H‐bonds in the loop and the β‐strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α‐helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β‐barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β‐strands, while αβ1 loops involve preferentially odd β‐strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to

ISSN:0887-3585    

DOI:10.1002/prot.340120402

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

年代:1992

数据来源: WILEY

摘要:

AbstractIn order to find rules for the secondary structure prediction of proteins which describe the (sequentially) long‐range interactions in sheet structures methods of applied graph theory were used. The so called β graph which describes the sheet topology was defined for every protein in the Brookhaven Data Bank containing β sheets. The resemblance of proteins at that topological level is discussed, and four notations and graphic representations of sheets which describe the sequential and topological neighborhoods of the strands were derived. This description level supports the usage of data structures which allow the implementation of efficient algorithms for the analysis and comparison of β structures in proteins. A computer program for the representation and retrieval of bibliographic data and β sheet structures was implemented. Some examples for substructure search illustrate the usefulness of the program. Two graphic catalogues were compiled: one contains all β graphs of PDB proteins and the other all occurring different greek key descri

ISSN:0887-3585    

DOI:10.1002/prot.340120403

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe packing of peptide helices in crystals of the leucine‐rich decapeptide Boc‐Aib‐Leu‐Aib‐Aib‐Leu‐Leu‐Leu‐Aib‐Leu‐Aib‐OMe provides an example of ladder‐like leucylleucyl interactions between neighboring molecules. The peptide molecule forms a helix with five 5→1 hydrogen bonds and two 4→1 hydrogen bonds near the C terminus. Three head‐to‐tail NH ċ O = C hydrogen bonds between helices form continuous columns of helices in the crystal. The helicial columns associate in an antiparallel fashion, except for the association of Leu ċ Leu side chains, which occurs along the diagonal of the cell where the peptide helices are parallel. The peptide, with formula C56H102N10O13, crystallizes in space group P212121with Z = 4 and cell parameters a = 16.774(3) Å, b = 20.032(3) Å and c = 20.117(3) Å; overall agreement factor R = 10.7% for 2014 da

ISSN:0887-3585    

DOI:10.1002/prot.340120404

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

年代:1992

数据来源: WILEY

摘要:

AbstractBased on the high‐resolution X‐ray crystallographic structure of phospholipase C fromBacillus cereus, the orientation of the phosphatidylcholine substrate in the active site of the enzyme is proposed. The proposal is based on extensive calculations using the GRID program and molecular mechanics geometry relaxations. The substrate model has been constructed by successively placing phosphate, choline and diacylglycerol moieties in the positions indicated from GRID calculations. On the basis of the resulting orientation of a complete phosphatidylcholine molecule, we propose a mechanism for the hydrolysis of the substr

ISSN:0887-3585    

DOI:10.1002/prot.340120405

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

年代:1992

数据来源: WILEY

摘要:

Abstractα‐Lytic protease, an extracellular bacterial serine protease, is synthesized with a large pro region that is required in vivo for the proper folding of the protease domain. To allow detailed mechanistic study, we have reconstituted pro region‐dependent folding in vitro. The pro region promotes folding of the protease domain in the absence of other protein factors or exogenous energy sources. Surprisingly, we find that the pro region is a high affinity inhibitor of the mature protease. The pro region also inhibits the closely relatedStreptomyces griseusprotease B, but not the more distantly related, yet structurally similar protease, elastase. Based on these data, we suggest a mechanism in which pro region binding reduces the free energy of a late folding transition state having native‐like str

ISSN:0887-3585    

DOI:10.1002/prot.340120406

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

年代:1992

数据来源: WILEY

摘要:

AbstractMethods have been developed to assess the stereochemical quality of any protein structure both globally and locally using various criteria. Several parameters can be derived from the coordinates of a given structure. Global parameters include the distribution of ϕ,ψ and χ1torsion angles, and hydrogen bond energies. There are clear correlations between these parameters and resolution; as the resolution improves, the distribution of the parameters becomes more clustered. These features show a broad distribution about ideal values derived from high‐resolution structures. Some structures have tightly clustered distributions even at relatively low resolutions, while others show abnormal scatter though the data go to high resolution. Additional indicators of local irregularity include proline ϕ angles, peptide bond planarities, disulfide bond lengths, and their χ3torsion angles. These stereochemical parameters have been used to generate measures of stereochemical quality which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution andR‐factor. The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates. A program suite is currently being developed which will quickly check a given structure, highlighting unusual stereochemistry and possibl

ISSN:0887-3585    

DOI:10.1002/prot.340120407

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

年代:1992

数据来源: WILEY

摘要:

AbstractParamecium tetraureliabehavioral mutantcam12displays a “fast‐2” behavioral phenotype: it fails to respond to Na+stimuli. Electrophysiologically, it lacks a Ca+ +‐dependent Na+current. Genetics and DNA sequencing showed the primary defect ofcam12to be in the calmodulin gene (Kink et al., 1990). To correlate calmodulin structure and function inParamecium, we elucidated the primary structure ofcam12calmodulin. Peptide sequencing confirmed the two point mutations predicted by the DNA sequence: a glycine‐to‐glutamate substitution at position 40 and an aspartate‐to‐asparagine substitution at position 50. Our results further showed that lysine 13 and lysine 115 were methylated normally incam12. It is likely that the electrophysiological abnormalities ofcam12are a direct reflection of the amino‐acid substitutions, as opposed to improper posttranslati

ISSN:0887-3585    

DOI:10.1002/prot.340120408

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

年代:1992

数据来源: WILEY

摘要:

AbstractUDP‐galactose 4‐epimerase catalyzes the conversion of UDP‐galactose to UDP‐glucose during normal galactose metabolism. The molecular structure of UDP‐galactose 4‐epimerase fromEscherichia colihas now been solved to a nominal resolution of 2.5 Å. As isolated fromE. coli, the molecule is a dimer of chemically identical subunits with a total molecular weight of 79,000. Crystals of the enzyme used for this investigation were grown as a complex with the substrate analogue, UDP‐benzene, and belonged to the space group P212121with unit cell dimensions ofa= 76.3 Å,b= 83.1 Å,c= 132.1 Å, and one dimer per asymmetric unit. An interpretable electron density map calculated to 2.5 Å resolution was obtained by a combination of multiple isomorphous replacement with six heavy atom derivatives, molecular averaging, and solvent flattening.Each subunit of epimerase is divided into two domains. The larger N‐terminal domain, composed of amino acid residues 1–180, shows a classic NAD+binding motif with seven strands of parallel β‐pleated sheet flanked on either side of α‐helices. The seventh strand of the β‐pleated sheet is contributed by amino acid residues from the smaller domain. In addition, this smaller C‐terminal domain, consisting of amino acid residues 181–338, contains three strands of β‐pleated sheet, two major α‐helices and one helical turn. The substrate analogue, UDP‐benzene, binds in the cleft located between the two domains with its phenyl ring in close proximity to the nicotinamide ring of NAD+. Contrary to the extensive biochemical literature suggesting that epimerase binds only one NAD+per functional dimer, the map clearly shows electron density for two nicotinamide cofactors binding in symmetry‐related positions in the dimer. Likewise, each subunit i

ISSN:0887-3585    

DOI:10.1002/prot.340120409

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe conditional probability, P(σ|x), is a statement of the probability that the value of σ will be found given the prior information that a value of x has been observed. Here σ represents any one of the secondary structure types, α, β, τ, and ρ for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N‐cap and C‐cap values; (4) Chou–Fasman conformational parameters for helix, Pα, for sheet, Pβ, and for turn, Pτ; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, Iα, for sheet, Iβ, for turn, I,τ, and for random structure, Iρ.Plots of P (σ|x) vs. x are demonstrated to provide information about the correlation between structure and attribute, σ and x. The separations between different P (σ|x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P (α|x), P (β|x), P (τ|x) and P (ρ|x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix>Pα» N‐cap>C‐cap ≈ Iα≈ Iτ. The information value for turns, Iτ, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: Iβ» Pβ≈ hydropathy>Iρ≈ hydrophobic moment assuming sheet.Three attributes, at their low values, were found to give significant discrimination for the absence of helix: Iα≈ Pα≈ hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: Pβ» Iτ≈ hydropathy. Indications of the absence of σ could be as useful f

ISSN:0887-3585    

DOI:10.1002/prot.340120410

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

年代:1992

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340120401

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

年代:1992

数据来源: WILEY