Protein engineering最新文献

{"title":"A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). I: Methodology.","authors":"Denis Znamenskiy,&nbsp;Jacques Chomilier,&nbsp;Khan Le Tuan,&nbsp;Jean-Paul Mornon","doi":"10.1093/protein/gzg140","DOIUrl":"https://doi.org/10.1093/protein/gzg140","url":null,"abstract":"<p><p>We present an algorithm that is able to propose compact models of protein 3D structures, only starting from the prediction of the nature and length of regular secondary structures. Helices are modeled by cylinders and sheets by helicoid surfaces, all strands of a sheet being considered as a single block. It means that relative topology of the strands inside one sheet is a prerequisite. Loops are only considered as constraints, given by the maximal distance between their Calpha extremities according to their sequence length. Unconnected regular secondary structures are reduced to a single point, the center of their hydrophobic faces. These centers are then repeatedly moved in order to obtain a compact hydrophobic core. To prevent secondary structures from interpenetrating, a repulsive term is introduced in the function whose minimization leads to the compact structure. This RUSSIA (Rigid Unconnected Secondary Structure Assembly) algorithm has the advantage of relying on a small number of variables and therefore many initial conformations can be tested. Flexibility is produced in the following way: helices or sheets are allowed to rotate around the direction leading to the center of the model; residues in a sheet can slide along the main direction of the strand where they are embedded. RUSSIA is fast and simple and it produces on a test set several neighbor good models with an r.m.s. to the native structures in the range 1.4-3.7 A. These models can be further treated by statistical potentials used in threading approaches in order to detect the best candidate. The limits of the present method are the following: small proteins with few secondary structures are excluded; multi domain proteins must be split into several compact globular domains from their sequences; sheets of more than five strands and completely buried helices are not treated. In this first paper the algorithm is developed and in Part II, which follows, some applications are presented and the program is evaluated.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"925-35"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and functional analysis of a truncated form of Saccharomyces cerevisiae ATP sulfurylase: C-terminal domain essential for oligomer formation but not for activity.","authors":"D J Lalor,&nbsp;T Schnyder,&nbsp;V Saridakis,&nbsp;D E Pilloff,&nbsp;A Dong,&nbsp;H Tang,&nbsp;T S Leyh,&nbsp;E F Pai","doi":"10.1093/protein/gzg133","DOIUrl":"https://doi.org/10.1093/protein/gzg133","url":null,"abstract":"ATP sulfurylase catalyzes the first step in the activation of sulfate by transferring the adenylyl-moiety (AMP approximately ) of ATP to sulfate to form adenosine 5'-phosphosulfate (APS) and pyrophosphate (PP(i)). Subsequently, APS kinase mediates transfer of the gamma-phosphoryl group of ATP to APS to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS) and ADP. The recently determined crystal structure of yeast ATP sulfurylase suggests that its C-terminal domain is structurally quite independent from the other domains, and not essential for catalytic activity. It seems, however, to dictate the oligomerization state of the protein. Here we show that truncation of this domain results in a monomeric enzyme with slightly enhanced catalytic efficiency. Structural alignment of the C-terminal domain indicated that it is extremely similar in its fold to APS kinase although not catalytically competent. While carrying out these structural and functional studies a surface groove was noted. Careful inspection and modeling revealed that the groove is sufficiently deep and wide, as well as properly positioned, to act as a substrate channel between the ATP sulfurylase and APS kinase-like domains of the enzyme.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"1071-9"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24411004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The distinct heme coordination environments and heme-binding stabilities of His39Ser and His39Cys mutants of cytochrome b5.","authors":"Wen-Hu Wang,&nbsp;Jun-Xia Lu,&nbsp;Ping Yao,&nbsp;Yi Xie,&nbsp;Zhong-Xian Huang","doi":"10.1093/protein/gzg134","DOIUrl":"https://doi.org/10.1093/protein/gzg134","url":null,"abstract":"<p><p>A gene mutant library containing 16 designed mutated genes at His39 of cytochrome b(5) has been constructed by using gene random mutagenesis. Two variants of cytochrome b(5), His39Ser and His39Cys mutant proteins, have been obtained. Protein characterizations and reactions were performed showing that these two mutants have distinct heme coordination environments: ferric His39Ser mutant is a high-spin species whose heme is coordinated by proximal His63 and likely a water molecule in the distal pocket, while ferrous His39Ser mutant has a low-spin heme coordinated by His63 and Ser39; on the other hand, the ferric His39Cys mutant is a low-spin species with His63 and Cys39 acting as two axial ligands of the heme, the ferrous His39Cys mutant is at high-spin state with the only heme ligand of His63. These two mutants were also found to have quite lower heme-binding stabilities. The order of stabilities of ferric proteins is: wild-type cytochrome b(5) >> His39Cys > His39Ser.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"1047-54"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24411001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure-function discrimination of the N- and C- catalytic domains of human angiotensin-converting enzyme: implications for Cl- activation and peptide hydrolysis mechanisms.","authors":"Andreas G Tzakos,&nbsp;Athanassios S Galanis,&nbsp;Georgios A Spyroulias,&nbsp;Paul Cordopatis,&nbsp;Evy Manessi-Zoupa,&nbsp;Ioannis P Gerothanassis","doi":"10.1093/protein/gzg122","DOIUrl":"https://doi.org/10.1093/protein/gzg122","url":null,"abstract":"<p><p>Human somatic angiotensin I-converting enzyme (sACE) has two active sites present in two sequence homologous protein domains (ACE_N and ACE_C) possessing several biochemical features that differentiate the two active sites (i.e. chloride ion activation). Based on the recently solved X-ray structure of testis angiotensin-converting enzyme (tACE), the 3D structure of ACE_N was modeled. Electrostatic potential calculations reveal that the ACE_N binding groove is significantly more positively charged than the ACE_C, which provides a first rationalization for their functional discrimination. The chloride ion pore for Cl2 (one of the two chloride ions revealed in the X-ray structure of tACE) that connects the external solution with the inner part of the protein was identified on the basis of an extended network of water molecules. Comparison of ACE_C with the X-ray structure of the prokaryotic ClC Cl(-) channel from Salmonella enterica serovar typhimurium demonstrates a common molecular basis of anion selectivity. The critical role for Cl2 as an ionic switch is emphasized. Sequence and structural comparison between ACE_N and ACE_C and of other proteins of the gluzincin family highlights key residues that could be responsible for the peptide hydrolysis mechanism. Currently available mutational and substrate hydrolysis data for both domains are evaluated and are consistent with the predicted model.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"993-1003"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings.","authors":"Simon Penel,&nbsp;R Gwilym Morrison,&nbsp;Paul D Dobson,&nbsp;Russell J Mortishire-Smith,&nbsp;Andrew J Doig","doi":"10.1093/protein/gzg147","DOIUrl":"https://doi.org/10.1093/protein/gzg147","url":null,"abstract":"<p><p>We analysed the length distributions of different types of beta-strand in a high resolution, non-homologous set of 500 protein structures, finding differences in their mean lengths. Antiparallel edge strands in strand-turn-strand motifs show a preference for an even number of residues. This propensity is enhanced if the length is corrected for beta-bulges, which insert an extra residue into the strand. Residues in antiparallel edge beta-strands alternate between being in hydrogen bonded and non-hydrogen bonded rings. Antiparallel edges with an even number of residues are more likely to have their final beta residue in a non-hydrogen bonded ring. This suggests that non-hydrogen bonded rings are intrinsically more stable than hydrogen bonded rings, perhaps because its side chain packing is closer. Therefore, we suggest that a simple way to increase beta-hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the strand.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"957-61"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis.","authors":"Eric Alsop,&nbsp;Melanie Silver,&nbsp;Dennis R Livesay","doi":"10.1093/protein/gzg131","DOIUrl":"https://doi.org/10.1093/protein/gzg131","url":null,"abstract":"<p><p>It has been known for some time that thermophilic proteins generally have increased numbers of non-covalent interactions (salt bridges, hydrogen bonds, etc.) compared with their mesophilic orthologs. Recently, anecdotal structural comparisons suggest that non-specific acid-base ion pairs on the protein surface can be an evolutionary efficient mechanism to increase thermostability. In this comprehensive structural analysis, we confirm this to be the case. Comparison of 127 orthologous mesophilic- thermophilic protein groups indicates a clear preference for stabilizing acid-base pairs on the surface of thermophilic proteins. Compared with positions in the core, stabilizing surface mutations are less likely to disrupt the tertiary structure, and thus more likely to be evolutionarily selected. Therefore, we believe that our results, in addition to being theoretically interesting, will facilitate identification of charge-altering mutations likely to increase the stability of a particular protein structure.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"871-4"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissection of the structural determinants involved in formation of the dimeric form of D-amino acid oxidase from Rhodotorula gracilis: role of the size of the betaF5-betaF6 loop.","authors":"Luciano Piubelli,&nbsp;Gianluca Molla,&nbsp;Laura Caldinelli,&nbsp;Mirella S Pilone,&nbsp;Loredano Pollegioni","doi":"10.1093/protein/gzg125","DOIUrl":"https://doi.org/10.1093/protein/gzg125","url":null,"abstract":"<p><p>The role of the long loop connecting beta-strands F5 and F6 (21 amino acids, Pro302-Leu-Asp-Arg-Thr-Lys-Ser-Pro-Leu-Ser-Leu-Gly-Arg-Gly-Ser-Ala-Arg-Ala-Ala-Lys-Glu322) present in Rhodotorula gracilis d-amino acid oxidase (RgDAAO) was investigated by site-directed mutagenesis. This loop was proposed to play an important role in the 'head-to-tail' monomer-monomer interaction of this dimeric flavoenzyme: in particular, by means of electrostatic interactions between positively charged residues of the betaF5-betaF6 loop of one monomer and negatively charged residues belonging to the alpha-helices I3' and I3\" of the other monomer. We produced a mutant of RgDAAO (namely, DAAO-DeltaLOOP2), in which only minor structural perturbations were introduced (only five amino acids were deleted; new sequence of the betaF5-betaF6 loop is Pro302-Leu-Asp-Arg-Thr-Leu-Gly-Arg-Gly-Ser-Ala-Arg-Ala-Ala-Lys-Glu317), and the charge of the betaF5-betaF6 loop not modified. The DeltaLOOP2 mutant is monomeric, has a weaker binding with the FAD cofactor, a decrease of the kinetic efficiency, and slight modifications in its spectral properties. The short version of the loop does not allow a correct monomer-monomer interaction, and its presence in the monomeric DAAO is a destabilizing structural element since the DeltaLOOP2 mutant is highly susceptible to proteolysis. These results, confirming the role of this loop in the subunits interaction and thus in stabilization of the sole dimeric form of RgDAAO, put forward the evidence that even a short deletion of the loop generates a consistent variation of the enzyme structure-function properties.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"1063-9"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24411003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recombinant porcine intestinal carboxylesterase: cloning from the pig liver esterase gene by site-directed mutagenesis, functional expression and characterization.","authors":"Anna Musidlowska-Persson,&nbsp;Uwe T Bornscheuer","doi":"10.1093/protein/gzg120","DOIUrl":"https://doi.org/10.1093/protein/gzg120","url":null,"abstract":"<p><p>It was shown recently that proline-beta-naphthylamidase from pig liver resembles the gamma-subunit of pig liver esterase (PLE), which could be functionally expressed in the yeast Pichia pastoris in recombinant form (rPLE). The gene encoding rPLE shares 97% identity with the published nucleotide sequence of porcine intestinal carboxylesterase (PICE). By site-directed mutagenesis, 22 nucleotides encoding 17 amino acids were exchanged stepwise from the PLE gene yielding the recombinant PICE sequence and eight intermediate mutants. All esterases were successfully produced in P.pastoris as extracellular proteins with specific activities ranging from 4 to 377 U/mg and V(max)/K(m) values from 12 to 1000 l min(-1) x 10(-3) using p-nitrophenyl acetate as substrate. Activity-staining of native polyacrylamide gels followed by molecular mass determination suggests that the most active forms of all variants are present as trimers with a molecular mass of 190-210 kDa. All enzymes exhibit the highest activity in the pH range 8-9 and between 60 and 70 degrees C. Almost all esterases show a higher ratio of methyl butyrate hydrolase activity to proline-beta-naphthylamidase activity than rPLE.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"1139-45"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A backbone-reversed all-beta polypeptide (retro-CspA) folds and assembles into amyloid nanofibres.","authors":"Anshuman Shukla,&nbsp;Manoj Raje,&nbsp;Purnananda Guptasarma","doi":"10.1093/protein/gzg142","DOIUrl":"https://doi.org/10.1093/protein/gzg142","url":null,"abstract":"<p><p>The backbone-reversed or 'retro', form of a model all-beta-sheet protein, Escherichia coli CspA, was produced from a synthetic gene in E.coli in fusion with an N-terminal affinity tag. Following purification under denaturing conditions and dialysis-based removal of urea, the protein was found to fold into a soluble, poorly structured multimer. Upon concentration, this state readily transformed into amyloid nanofibres. Congo Red-binding amorphous forms were also observed. Since a beta-sheet-forming sequence is expected to retain high beta-sheet-forming propensity even after backbone reversal and given the fact that folding of retro-CspA occurs only to a poorly structured form, we conclude that the increase effected in protein concentration may be responsible for the formation of intermolecular beta-sheets, facilitating the bleeding away of the protein's conformational equilibrium into aggregates that generate well-formed fibres. Since every molecule in these fibres contains a peptide tag for binding Ni(2+), the fibres may provide a template for deposition of nickel to generate novel materials.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"875-9"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). II: Applications.","authors":"Denis Znamenskiy,&nbsp;Khan Le Tuan,&nbsp;Jean-Paul Mornon,&nbsp;Jacques Chomilier","doi":"10.1093/protein/gzg141","DOIUrl":"https://doi.org/10.1093/protein/gzg141","url":null,"abstract":"<p><p>The RUSSIA procedure (Rigid Unconnected Secondary Structure Iterative Assembly) produces structural models of cores of small- and medium-sized proteins. Loops are omitted from this treatment and regular secondary structures are reduced to points, the centers of their hydrophobic faces. This methodology relies on the maximum compactness of the hydrophobic residues, as described in detail in Part I. Starting data are the sequence and the predicted limits and natures of regular secondary structures (alpha or beta). Helices are treated as rigid cylinders, whereas beta-strands are collectively taken into account within beta-sheets modeled by helicoid surfaces. Strands are allowed to shift along their mean axis to allow some flexibility and the alpha-helices can be placed on either side of beta-sheets. Numerous initial conformations are produced by discrete rotations of the helices and sheets around the direction going from the center of their hydrophobic face to the global center of the protein. Selection of proposed models is based upon a criterion lying on the minimization of distances separating hydrophobic residues belonging to different regular secondary structures. The procedure is rapid and appears to be robust relative to the quality of starting data (nature and length of regular secondary structures). This dependence of the quality of the model on secondary structure prediction and in particular the beta-sheet topology, is one of the limits of the present algorithm. We present here some results for a set of 12 proteins (alpha, beta and alpha/beta classes) of lengths 40-166 amino acids. The r.m.s. deviations for core models with respect to the native proteins are in the range 1.4-3.7 A.</p>","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 12","pages":"937-48"},"PeriodicalIF":0.0,"publicationDate":"2003-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24410585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}