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Yadav PK, Antonyraj CB, Basheer Ahamed SI, Srinivas S. Understanding Russell's viper venom factor V activator's substrate specificity by surface plasmon resonance and in-silico studies. PLoS One 2017; 12:e0181216. [PMID: 28732041 PMCID: PMC5521794 DOI: 10.1371/journal.pone.0181216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/28/2017] [Indexed: 11/18/2022] Open
Abstract
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids. Our investigation for justifying the binding efficacy and kinetics of peptides includes SPR method, protein-peptide docking, molecular dynamics simulation, and principal component analysis (PCA). Surprisingly, the SPR experiment disclosed that the Peptide II showed a lower binding affinity with KD of 2.775 mM while the Peptide I showed none. Docking and simulation of both the peptides with RVV-V engaged either rooted or shallow binding for Peptide II and Peptide I respectively. The peptide binding resulted in global conformational changes in the native fold of RVV-V, whereas the similar studies for thrombin failed to make major changes in the native fold. In support, the PCA analysis for RVV-V showed the dislocation of catalytic triad upon binding both the peptides. Hence, RVV-V, a serine protease, is incompetent in cleaving these two sites. This study suggests a transition in RVV-V from the native rigid to the distorted flexible structure and paves a way to design a new peptide substrate/inhibitor.
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Affiliation(s)
- Pradeep K. Yadav
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | | | | | - Sistla Srinivas
- GE Healthcare Life Sciences, John F Welch Technology Centre, EPIP, Bengaluru, India
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Wu F, Zhao M, Zhang Y, Su N, Xiong Z, Xu P. Recombinant acetylated trypsin demonstrates superior stability and higher activity than commercial products in quantitative proteomics studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1059-1066. [PMID: 27003043 DOI: 10.1002/rcm.7535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/31/2016] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Trypsin is an important digestive enzyme in peptide sample preparation for proteomics. It digests proteins at the C-terminal of Arg or Lys residues. The majority of commercial products are obtained from animal sources. In a previous study, we reported the production process for recombinant trypsin (r-trypsin) and acetylated trypsin (r-Ac-trypsin). In this paper, we want to evaluate whether the r-trypsin and r-Ac-trypsin are suitable for proteomics research. METHODS The trypsins used in this research were first normalized to the same concentration and used for further evaluation. The stability and buffer compatibility (2M urea, 0.1% SDS and 10% acetonitrile) were compared and visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The digestion efficiency and specificity were compared based on a simple protein substrate, human serum albumin (HSA) and a complex proteomic sample, yeast lysate. The acquisition of proteomics data was achieved by ultra-high performance liquid chromatography (UPLC) connected to an LTQ Orbitrap Velos mass spectrometer. RESULTS r-Ac-trypsin demonstrated similar tolerance to 2 M urea and 10% acetonitrile but weaker 0.1% SDS tolerance than commercial trypsins. Based on simple protein sample HSA, the activity and specificity of r-Ac-trypsin were similar to that of commercial trypsins. However, it demonstrated superior activity and specificity on complicated samples like yeast lysate. More interestingly, the newly developed r-Ac-trypsin was more resistant to autolysis, which enabled more complete digestion of proteomic samples. CONCLUSIONS The r-Ac-trypsin described here is a recombinant product. In addition it showed similar or superior properties such as stability activity and specificity to commercial products. It can be used in peptide sample preparation in proteomics studies.
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Affiliation(s)
- Feilin Wu
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Mingzhi Zhao
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Su
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Zhi Xiong
- Life Science College, Southwest Forestry University, Kunming, 650224, P.R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, 102206, P.R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P.R. China
- Anhui Medical University, Hefei, 230032, Anhui, P.R. China
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Kinjo AR, Nakamura H. Comprehensive structural classification of ligand-binding motifs in proteins. Structure 2009; 17:234-46. [PMID: 19217394 DOI: 10.1016/j.str.2008.11.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 11/10/2008] [Accepted: 11/13/2008] [Indexed: 11/15/2022]
Abstract
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and universality of ligand-binding sites in protein structures, we conducted the all-against-all atomic-level structural comparison of over 180,000 ligand-binding sites found in all the known structures in the Protein Data Bank by using a recently developed database search and alignment algorithm. By applying a hybrid top-down-bottom-up clustering analysis to the comparison results, we determined approximately 3000 well-defined structural motifs of ligand-binding sites. Apart from a handful of exceptions, most structural motifs were found to be confined within single families or superfamilies, and to be associated with particular ligands. Furthermore, we analyzed the components of the similarity network and enumerated more than 4000 pairs of structural motifs that were shared across different protein folds.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Guo XL, Li L, Wei DQ, Zhu YS, Chou KC. Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids 2008; 35:375-82. [PMID: 18235997 PMCID: PMC7088033 DOI: 10.1007/s00726-007-0611-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 09/23/2007] [Indexed: 01/05/2023]
Abstract
The cleavage property of hemagglutinin (HA) by different proteases was the prime determinant for influenza A virus pathogenicity. In order to understand the cleavage mechanism, molecular modeling tools were utilized to study the coupled model systems of the proteases, i.e., trypsin and furin and peptides of the cleavage sites specific to H5N1 and H1 HAs, which constitute models of HA precursor in complex with cleavage proteases. The peptide segments ‘RERRRKKR ↓ G’ and ‘SIQSR ↓ G’ from the high pathogenic H5N1 H5 and the low pathogenic H1N1 H1 cleavage sites were docking to the trypsin and furin active pockets, respectively. It was observed through the docking studies that trypsin was able to recognize and cleave both the high pathogenic and low pathogenic hemagglutinin, while furin could only cleave the high pathogenic hemagglutinin. An analysis of binding energies indicated that furin got most of its selectivity due to the interactions with P1, P4, and P6, while having less interaction with P2 and little interactions with P3, P5, P7, and P8. Some mutations of H5N1 H5 cleavage sequence fitted less well into furin and would reduce high pathogenicity of the virus. These findings hint that we should focus at the subsites P1, P4, and P6 for developing drugs against H5N1 viruses.
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Affiliation(s)
- X-L Guo
- College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Syed Ibrahim B, Pattabhi V. Trypsin inhibition by a peptide hormone: crystal structure of trypsin-vasopressin complex. J Mol Biol 2005; 348:1191-8. [PMID: 15854654 DOI: 10.1016/j.jmb.2005.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/07/2005] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
The large variety of serine protease inhibitors, available from various sources such as tissues, microorganisms, plants, etc., play an important role in regulating the proteolytic enzymes. The analysis of protease-inhibitor complexes helps in understanding the mechanism of action, as well as in designing inhibitors. Vasopressin, an anti-diuretic nonapeptide hormone, is found to be an effective inhibitor of trypsin, with a K(i) value of 5 nM. The crystal structure of the trypsin-vasopressin complex revealed that vasopressin fulfils all the important interactions for an inhibitor, without any break in the scissile peptide bond. The cyclic nature due to a disulfide bridge between Cys1 and Cys6 of vasopressin provides structural rigidity to the peptide hormone. The trypsin-binding site is located at the C terminus, while the neurophysin-binding site is at the N terminus of vasopressin. This study will assist in designing new peptide inhibitors. This study suggests that vasopressin inhibition of trypsin may have unexplored biological implications.
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Affiliation(s)
- B Syed Ibrahim
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
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