摘要:

AbstractA computer program is described that produces a description of the secondary structure and supersecondary structure of a polypeptide chain using the list of alpha carbon coordinates as input. Restricting the term “secondary structure” to the conformation ofcontiguous segmentsof the chain, the program determines the initial and final residues in helices, extended strands, sharp turns, and omega loops. This is accomplished through the use of difference distance matrices. The distances in idealized models of the segments are compared with the actual structure, and the differences are evaluated for agreement within preset limits. The program assigns 90–95% of the residues in most proteins to at least one type of secondary elementIn a second step the now‐defined helices and strands are idealized as straight line segments, and the axial directions and locations are compiled from the input Cα coordinate list. These data are used to check for moderate curvature in strands and helices, and the secondary structure list is corrected where necessary. The geometric relations between these line segments are then calculated and output as the first level of supersecondary structure. A maximum of six parameters are required for a complete description of the relations between each pair. Frequently a less complete description will suffice, for example just the interaxial separation and angle. Both the secondary structure and one aspect of the supersecondary structure can be displayed in a character matrix analogous to the distance matrix format. This allows a quite accurate two‐dimensional display of the three‐dimensional structure, and several examples are presentedA procedure for searching for arbitrary substructures in proteins using distance matrices is also described. A search for the DNA binding helix‐turnhelix motif in the Protein Data Bank serves as an exampleA further abstraction of the above data can be made in the form of a metamatrix where each diagonal element represents an entire secondary segment rather than a single atom, and the off‐diagonal elements contain all the parameters describing their interrelations. Such matrices can be used in a straightforward search for higher levels of supersecondary structure or used in toto as a representation of the entire tertiary structure of the p

ISSN:0887-3585    

DOI:10.1002/prot.340030202

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

年代:1988

数据来源: WILEY

摘要:

AbstractThe Lys binding site of kringle 1 and 4 (K1 and K4) of plasminogen (PG) has been modeled on the basis of the three‐dimensional structure of kringle 1 of prothrombin and 300‐ and 600‐MHz proton nuclear magnetic resonance observations. These structures were then compared to the corresponding regions of modeled kringle 1 and 2 of tissue plasminogen activator (PA). The coordinates of the modeled structures have been refined by energy minimization in the presence and absence of ϵ‐aminocaproic acid ligand in order basically to remove unacceptable van der Waals contacts. The binding site is characterized by an apparent dipolar surface, the polar parts of which are separated by a hydrophobic region of highly conserved aromatic residues. Zwitterionic ligands such as Lys and ϵ‐aminocaproic acid form ion pair interactions with Asp55 and Asp57 located on the dipolar surface; the latter are also conserved in all the Lys binding kringles. The cationic center of the dipolar surface is Arg71, in the case of PGK4, and is composed of Arg34 and Arg71 in PGK1. The doubly charged anionic/cationic interaction centers of the latter might account for the larger binding constants of PGK1 for like‐ligands but the modeling suggests that PGK4 might be kinetically faster in binding bulkier ligands. The binding site region of PAK2, which also binds Lys, resembles those of PGK1 and PGK4. Since PAK2 lacks both cationic center Arg residues, ligand carboxylate binding appears to be accomplished though an imidazolium ion of His64, which is located just below the outer surface o

ISSN:0887-3585    

DOI:10.1002/prot.340030203

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

年代:1988

数据来源: WILEY

摘要:

AbstractIn an effort to identify the structural elements essential to a given protein function a new pattern‐directed inference system has been developed. It has been employed to identify a potential dinucleotide‐binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subu

ISSN:0887-3585    

DOI:10.1002/prot.340030204

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

年代:1988

数据来源: WILEY

摘要:

AbstractThe Trg protein is one of a family of transducer proteins that mediate chemotactic response inEscherichia coli. Transducers are methylaccepting proteins that gain or lose methyl esters on specific glutamyl residues during sensory adaptation. In this study, the significance of multiple sites of methylation on transducer proteins was addressed by using oligonucleotide‐directed, site‐specific mutagenesis to substitute an alanyl residue at each of the five methyl‐accepting sites in Trg. The resulting collection of five mutations, each inactivating a single site, was analyzed for effects on covalent modification at the remaining sites on Trg and for the ability of the altered proteins to mediate sensory adaptation. Most of the alanyl substitutions had substantial biochemical effects, enhancing or reducing methyl‐accepting activity of other sites, including one case of activation of a site not methylated in wild‐type protein. Analysis of the altered proteins provided explanations for many features of the complex pattern of electrophoretic forms exhibited by Trg. The mutant proteins were less efficient than normal Trg in mediating adaptation. Correlation of biochemical and behavioral data indicated that reduction in the number of methyl‐accepting sites on the transducer lengthened the time required to reach an ad

ISSN:0887-3585    

DOI:10.1002/prot.340030205

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

年代:1988

数据来源: WILEY

摘要:

AbstractHuman myeloperoxidase and human thyroid peroxidase nucleotide and amino acid sequences were compared. The global similarities of the nucleotide and amino acid sequences are 46% and 44%, respectively. These similarities are most evident within the coding sequence, especially that encoding the myeloperoxidase functional subunits. These results clearly indicate that myeloperoxidase and thyroid peroxidase are members of the same gene family and diverged from a common ancestral gene. The residues at 416 in myeloperoxidase and 407 in thyroid peroxidase were estimated as possible candidates for the proximal histidine residues that link to the iron centers of the enzymes. The primary structures around these histidine residues were compared with those of other known peroxidases. The similarity in this region between the two animal peroxidases (amino acid 396–418 in thyroid peroxidase and 405–427 in myeloperoxidase) is 74%; however, those between the animal peroxidases and other yeast and plant peroxidases are not significantly high, although several conserved features have been observed. The possible location of the distal histidine residues in myeloperoxidase and thyroid peroxidase amino acid sequences are also discus

ISSN:0887-3585    

DOI:10.1002/prot.340030206

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

年代:1988

数据来源: WILEY

摘要:

AbstractThe gene for human interleukin‐1β was cloned from SK‐hep‐1 hepatoma cellular RNA and expressed at high levels inEscherichia coliboth as the naturally processed form (rIL‐1β) and as a variant with an additional sequence of three amino acids on the N‐terminus (rIL‐1β+). Expressed protein was purified to homogeneity by a sequence of steps, which included low pH incubation, adsorption and desorption from Procion Red Sepharose, sizing on a Superose 12 fast‐performance liquid chromatography (FPLC) column, and anion exchange chromatography on QAE Sepharose. The final step provided a biologically active protein that migrates on twodimensional (2‐D) gels as a single spot with a pI of 6.7 ± 0.2 and a molecular mass of 17,500 daltons. Concentrated solutions of rIL‐1β have produced crystals by ammonium sulfate precipitation. The crystals are tetragonal, show the symmetry of space group P41or its enantiomer, have lattice constants of a = 58.46 (1) and c = 77.02 (3) A, and scatter to at least 2 Å resolution. A structure determination based on thes

ISSN:0887-3585    

DOI:10.1002/prot.340030207

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

年代:1988

数据来源: WILEY

摘要:

AbstractChymotrypsin modified with polyethylene glycol was successfully used for peptide synthesis in organic solvents. The benzene‐soluble modified enzyme readily catalyzed both aminolysis of N‐benzoyl‐L‐tyrosine p‐nitroanilide and synthesis of N‐benzoyl‐L‐tyrosine butylamide in the presence of trace amounts of water. A quantitative reaction was obtained when either hydrophobic or bulky amides of L‐ as well as D‐amino acids were used as acceptor nucleophiles, while almost no reaction occurred with free amino acids or ester derivativesThe acceptor nucleophile specificity of modified chymotrypsin as a catalyst in the formation of both amide and peptide bonds in organic solvents was quite comparable to that in aqueous solution as well as to that of the leaving group in hydrolysis reactions. By contrast, the substrate specificity of modified chymotrypsin in organic solvents was different from that in water since arginine and lysine esters were found to be as effective as aromatic amino acids to form the acyl‐enzyme with subsequent synthe

ISSN:0887-3585    

DOI:10.1002/prot.340030208

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

年代:1988

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340030201

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

年代:1988

数据来源: WILEY