Protein engineering最新文献_第7页

Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues. 大豆β-淀粉酶表面氨基酸残基替代突变体晶体结构的变化。

Protein engineering Pub Date : 2003-11-01 DOI: 10.1093/protein/gzg109

You-Na Kang, Motoyasu Adachi, Bunzo Mikami, Shigeru Utsumi

{"title":"Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues.","authors":"You-Na Kang, Motoyasu Adachi, Bunzo Mikami, Shigeru Utsumi","doi":"10.1093/protein/gzg109","DOIUrl":"10.1093/protein/gzg109","url":null,"abstract":"In spite of the high similarity of amino acid sequence and three-dimensional structure between soybean beta-amylase (SBA) and sweet potato beta-amylase (SPB), their quaternary structure is quite different, being a monomer in SBA and a tetramer in SPB. Because most of the differences in amino acid sequences are found in the surface region, we tested the tetramerization of SBA by examining mutations of residues located at the surface. We designed the SBA tetramer using the SPB tetramer structure as a model and calculating the change of accessible surface area (DeltaASA) for each residue in order to select sites for the mutation. Two different mutant genes encoding SB3 (D374Y/L481R/P487D) and SB4 (K462S added to SB3), were constructed for expression in Escherichia coli and the recombinant proteins were purified. They existed as a monomer in solution, but gave completely different crystals from the native SBA. The asymmetric unit of the mutants contains four molecules, while that of native SBA contains one. The interactions of the created interfaces revealed that there were more intermolecular interactions in the SB3 than in the SB4 tetramer. The substituted charged residues on the surface are involved in interactions with adjacent molecules in a different way, forming a new crystal packing pattern.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 11","pages":"809-17"},"PeriodicalIF":0.0,"publicationDate":"2003-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24088074","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}

引用次数: 5

Exploring the sequence patterns in the alpha-helices of proteins. 探索蛋白质α螺旋的序列模式。

Protein engineering Pub Date : 2003-11-01 DOI: 10.1093/protein/gzg101

Junwen Wang, Jin-An Feng

{"title":"Exploring the sequence patterns in the alpha-helices of proteins.","authors":"Junwen Wang, Jin-An Feng","doi":"10.1093/protein/gzg101","DOIUrl":"https://doi.org/10.1093/protein/gzg101","url":null,"abstract":"This paper reports an extensive sequence analysis of the alpha-helices of proteins. alpha-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long alpha-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for alpha-helical conformations. It was shown that the amino acid pair preference for alpha-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for alpha-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential 'codes' for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 11","pages":"799-807"},"PeriodicalIF":0.0,"publicationDate":"2003-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24088073","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}

引用次数: 41

Structural diversity in the small heat shock protein superfamily: control of aggregation by the N-terminal region. 小热休克蛋白超家族的结构多样性:n端区域对聚集的控制。

Protein engineering Pub Date : 2003-11-01 DOI: 10.1093/protein/gzg102

John C Salerno, Cheryl L Eifert, Kathleen M Salerno, Jane F Koretz

引用次数: 17

On the rotational operators in protein structure simulations. 蛋白质结构模拟中的旋转算子研究。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg092

Carlos Alvarado, Kazem Kazerounian

{"title":"On the rotational operators in protein structure simulations.","authors":"Carlos Alvarado, Kazem Kazerounian","doi":"10.1093/protein/gzg092","DOIUrl":"https://doi.org/10.1093/protein/gzg092","url":null,"abstract":"The reduction of the computational complexity of the algorithms dealing with protein structure analysis and conformation predictions is of prime importance. One common element in most of these algorithms is the process of transforming geometrical information between dihedral angles and Cartesian coordinates of the atoms in the protein using rotational operators. In the literature, the operators used in protein structures are rotation matrices, quaternions in vector and matrix forms and the Rodrigues-Gibbs formula. In the protein structure-related literature, the most widely promoted rotational operator is the quaternions operator. In this work, we studied the computational efficiency of the mathematical operations of the above rotational operators applied to protein structures. A similar study applied to protein structures has not been reported previously. We concluded that the computational efficiency of these rotational operators applied to protein chains is different from those reported for other applications (such as mechanical machinery) and the conclusions are not analogous. Rotation matrices are the most efficient mathematical operators in the protein chains. We examined our findings in two protein molecules: Ab1 tyrosine kinase and heparin-binding growth factor 2. We found that the rotation matrix operator has between 2 and 187% fewer mathematical operations than the other rotational operators.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 10","pages":"717-20"},"PeriodicalIF":0.0,"publicationDate":"2003-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24060759","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}

引用次数: 14

A novel fingerprint for the characterization of protein folds. 一种新的蛋白质折叠特征指纹图谱。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg100

Mihaly Mezei

引用次数: 7

Fine mapping and structural analysis of immunodominant IgE allergenic epitopes in chicken egg ovalbumin. 鸡卵白蛋白免疫显性IgE致敏表位精细定位及结构分析。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg095

Yoshinori Mine, Prithy Rupa

引用次数: 69

Common active site architecture and binding strategy of four phenylpropanoid P450s from Arabidopsis thaliana as revealed by molecular modeling. 拟南芥中4种苯丙类p450的共同活性位点结构及结合策略

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg094

Sanjeewa Rupasinghe, Jerome Baudry, Mary A Schuler

{"title":"Common active site architecture and binding strategy of four phenylpropanoid P450s from Arabidopsis thaliana as revealed by molecular modeling.","authors":"Sanjeewa Rupasinghe, Jerome Baudry, Mary A Schuler","doi":"10.1093/protein/gzg094","DOIUrl":"https://doi.org/10.1093/protein/gzg094","url":null,"abstract":"Despite extensive primary sequence diversity, crystal structures of several bacterial cytochrome P450 monooxygenases (P450s) and a single eukaryotic P450 indicate that these enzymes share a structural core of alpha-helices and beta-sheets and vary in the loop regions contacting individual substrates. To determine the extent to which individual structural features are conserved among divergent P450s existing in a single biosynthetic pathway, we have modeled the structures of four highly divergent P450s (CYP73A5, CYP84A1, CYP75B1, CYP98A3) in the Arabidopsis phenylpropanoid pathway synthesizing lignins, flavonoids and anthocyanins. Analysis of these models has indicated that, despite primary sequence identities as low as 13%, the structural cores and several loop regions of these P450s are highly conserved. Substrate docking indicated that all four enzymes employ a common strategy to identify their substrates in that their cinnamate-derived substrates align along helix I with their aromatic ring positioned towards the C-terminus of this helix and their aliphatic tails positioned towards the N-terminus. Further similarity was observed in the way the substrates contact the consensus P450 substrate recognition sites (SRS). Residues predicted to contact the aromatic ring region exist in SRS5, SRS6 and the C-terminal portion of SRS4 and residues contacting the distal end of each substrate exist in SRS1, SRS2 and the N-terminal portion of SRS4. Alignments of the regions contacting the aromatic ring region indicate that SRS4, SRS5 and SRS6 share higher degrees of sequence conservation than found in SRS1, SRS2 or the full-length protein.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 10","pages":"721-31"},"PeriodicalIF":0.0,"publicationDate":"2003-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24060760","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}

引用次数: 65

Structure-based substitutions for increased solubility of a designed protein. 以结构为基础的取代以增加所设计蛋白质的溶解度。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg098

Leila K Mosavi, Zheng-Yu Peng

{"title":"Structure-based substitutions for increased solubility of a designed protein.","authors":"Leila K Mosavi, Zheng-Yu Peng","doi":"10.1093/protein/gzg098","DOIUrl":"https://doi.org/10.1093/protein/gzg098","url":null,"abstract":"Manipulation of protein solubility is important for many aspects of protein design and engineering. Previously, we designed a series of consensus ankyrin repeat proteins containing one, two, three and four identical repeats (1ANK, 2ANK, 3ANK and 4ANK). These proteins, particularly 4ANK, are intended for use as a universal scaffold on which specific binding sites can be constructed. Despite being well folded and extremely stable, 4ANK is soluble only under acidic conditions. Designing interactions with naturally occurring proteins requires the designed protein to be soluble at physiological pH. Substitution of six leucines with arginine on exposed hydrophobic patches on the surface of 4ANK resulted in increased solubility over a large pH range. Study of the pH dependence of stability demonstrated that 4ANK is one of the most stable ankyrin repeat proteins known. In addition, analogous leucine to arginine substitutions on the surface of 2ANK allowed the partially folded protein to assume a fully folded conformation. Our studies indicate that replacement of surface-exposed hydrophobic residues with positively charged residues can significantly improve protein solubility at physiological pH.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 10","pages":"739-45"},"PeriodicalIF":0.0,"publicationDate":"2003-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24060762","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}

引用次数: 76

Chimeric ribonuclease as a source of human adapter protein for targeted drug delivery. 嵌合核糖核酸酶作为靶向药物递送的人适配蛋白来源。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg097

Timur I Gaynutdinov, Eugene Myshkin, Joseph M Backer, Marina V Backer

{"title":"Chimeric ribonuclease as a source of human adapter protein for targeted drug delivery.","authors":"Timur I Gaynutdinov, Eugene Myshkin, Joseph M Backer, Marina V Backer","doi":"10.1093/protein/gzg097","DOIUrl":"https://doi.org/10.1093/protein/gzg097","url":null,"abstract":"Assembled modular complexes for targeted drug delivery can be based on strong non-covalent interactions between a cargo module containing an adapter protein and a docking tag fused to a targeting protein. We have recently constructed a completely humanized adapter/docking tag system based on interactions between 15 amino acid (Hu-tag) and 110 amino acid (HuS) fragments of human ribonuclease I (RNase I). Although recombinant HuS can be expressed and refolded into a functionally active form, the purification procedure is cumbersome and expensive, and more importantly, it yields a significant proportion of improperly folded proteins. Here we describe engineering, high-yield expression, and purification of a chimeric bovine/human RNase (BH-RNase) comprising 1-29 N-terminal amino acids of bovine ribonuclease A and 30-127 amino acids of human RNase I. Unlike RNase I, the chimeric BH-RNase can be cleaved by either subtilisin or proteinase K between A20 and S21, providing a functionally active HuS. The HuS obtained from chimeric BH-RNase differs from wild-type HuS by an N24T substitution; therefore, we have reverted this substitution by mutating N24 to T24 in BH-RNase. This BH-RNase mutant can also be cleaved by subtilisin or proteinase K yielding wild-type HuS. The affinity of HuS obtained from BH-RNase to Hu-tag is approximately five times higher than that for recombinant HuS, reflecting a higher percentage of properly folded proteins.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 10","pages":"771-5"},"PeriodicalIF":0.0,"publicationDate":"2003-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg097","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24060645","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}

引用次数: 6

Role of the tyrosine corner motif in the stability of neocarzinostatin. 酪氨酸角基序在新羧抑素稳定性中的作用。

Protein engineering Pub Date : 2003-10-01 DOI: 10.1093/protein/gzg099

Magali Nicaise, Marielle Valerio-Lepiniec, Nadia Izadi-Pruneyre, Elisabeth Adjadj, Philippe Minard, Michel Desmadril

{"title":"Role of the tyrosine corner motif in the stability of neocarzinostatin.","authors":"Magali Nicaise, Marielle Valerio-Lepiniec, Nadia Izadi-Pruneyre, Elisabeth Adjadj, Philippe Minard, Michel Desmadril","doi":"10.1093/protein/gzg099","DOIUrl":"https://doi.org/10.1093/protein/gzg099","url":null,"abstract":"Although the immunoglobulin-like beta-sandwich fold has no specifically conserved function, some common structural features have been observed, in particular a structural motif, the tyrosine corner. Such a motif was described in neocarzinostatin (NCS), a bacterial protein the structure of which is very similar to that of the immunoglobulin domain. Compared with the other beta-sheet proteins, the NCS 'tyrosine corner' presents non-standard structural features. To investigate the role of this motif in the NCS structure and stability, we studied the properties of a mutant where the H bond interaction had been eliminated by replacing the tyrosine with a phenylalanine. This mutation costs 4.0 kcal/mol showing that the NCS 'tyrosine corner' is involved in protein stability as in the other Greek key proteins. This destabilization is accompanied by remote structural effects, including modification of the binding properties, suggesting an increase in the internal flexibility of the protein. With a view to using this protein for drug targeting, these results along with those obtained previously allow us to define clearly the limitations of the modifications that can be performed on this scaffold.","PeriodicalId":20902,"journal":{"name":"Protein engineering","volume":"16 10","pages":"733-8"},"PeriodicalIF":0.0,"publicationDate":"2003-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/protein/gzg099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24060761","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}

引用次数: 10