{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,8]],"date-time":"2025-07-08T04:04:10Z","timestamp":1751947450688,"version":"3.41.2"},"reference-count":45,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100015747","name":"University Grants Commission","doi-asserted-by":"publisher","award":["19\/06\/2016(i)"],"award-info":[{"award-number":["19\/06\/2016(i)"]}],"id":[{"id":"10.13039\/100015747","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100021014","name":"Department of Science and Technology","doi-asserted-by":"publisher","award":["SR\/SO\/BB-29\/2010"],"award-info":[{"award-number":["SR\/SO\/BB-29\/2010"]}],"id":[{"id":"10.13039\/100021014","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We screened a random peptide phage display library using Russell\u2019s viper venom phospholipase A2 (RV-PLA2) as bait. Sequence information from the resulting set of bio-panned heptapeptides was analyzed and mined to determine likely sites of interaction between two subunits of RV-PLA2 homo dimers and between RV-PLA2 and the \u03b3PLA2 inhibitor PIP from Malayopython reticulatus. This was accomplished in part by sequence alignment of the affinity-selected peptides with the sequences of RV-PLA2 and PIP. Because similarity scores calculated from sequence alignments proved inadequate to determine interaction interfaces accurately for RV-PLA2 dimers, we explored the use of amino acid frequency-based interactions scores (SFI\/SFIN) for a more accurate prediction of protein\u2013protein interaction sites. Heptamers with elevated SFI(N) scores were compared to interfaces of interaction observed in crystal structures of RV-PLA2 homodimers and to sites of interaction predicted by protein\u2013protein docking between structures of RV-PLA2 and model of PIP. Segments with a high density of protein\u2013protein contacts coincided with heptamer sequences exhibiting SFI and\/or SFIN scores significantly above average, in both RV-PLA2 homodimers and in RV-PLA2 \u03b3PLI heteromeric structures. Elevated SFI and SFIN scores were associated with peptide function since the heptamers with some of the highest SFI and SFI(N) scores, LPGLPLS, GLPLSLQ and SLQNGLY constitute the known PLA2 inhibitor P-PB.I (LPGLPLSLQNGLY) while KLGRVDI, and WDGVYIR, constitute PIP-17 (LGRVDIHVWDGVYIRGR), IC50 for hsPLA2: 5.3\u00a0\u03bcM. A graph showing the alignment of maxima between SFI scores and average solvent accessibility (per heptamer) suggests that solvent accessibility is a major driver of both protein\u2013protein interaction and phage selection.<\/jats:p>\n               <jats:p>Insights We show by computational methods that in sets of small phage-displayed peptides of the same length selected for binding to the same target protein, amino acids contributing to binding at a particular position occur at higher frequencies than in random peptides. This position-specific selection of particular amino acids can be detected in the position-specific amino acid frequency distribution of that set of selected peptides. Therefore, when this position-specific amino acid frequency is mapped back onto a particular amino acid sequence of the same length, the sum of these frequencies can function as a measure of enrichment of selected amino acids.<\/jats:p>","DOI":"10.1093\/intbio\/zyaf012","type":"journal-article","created":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T05:24:36Z","timestamp":1751865876000},"source":"Crossref","is-referenced-by-count":0,"title":["Prediction of protein\u2013protein interaction sites between Russell\u2019s viper PLA2 and the \u03b3-phospholipase inhibitor PIP from the amino acid frequency distribution of a bio-panned peptide set"],"prefix":"10.1093","volume":"17","author":[{"given":"Karthika","family":"Rajan","sequence":"first","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham , Amritapuri Campus, Clappana P.O., Kollam, Kerala 690 525 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2638-1005","authenticated-orcid":false,"given":"Margaret","family":"Reick","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham , Amritapuri Campus, Clappana P.O., Kollam, Kerala 690 525 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4370-8183","authenticated-orcid":false,"given":"Aswathy","family":"Alangode","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham , Amritapuri Campus, Clappana P.O., Kollam, Kerala 690 525 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3390-9266","authenticated-orcid":false,"given":"Martin","family":"Reick","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham , Amritapuri Campus, Clappana P.O., Kollam, Kerala 690 525 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,7,7]]},"reference":[{"key":"2025070701243308700_ref1","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1580\/06-WEME-CO-023R1.1","article-title":"Snakes of medical importance in India: is the concept of the \"big 4\" still relevant and useful?","volume":"18","author":"Simpson","year":"2007","journal-title":"Wilderness Environ Med"},{"key":"2025070701243308700_ref2","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1080\/14789450.2018.1528150","article-title":"Proteomic analysis reveals geographic variation in venom composition of Russell's viper in the Indian subcontinent: implications for clinical manifestations post-envenomation and antivenom treatment","volume":"15","author":"Kalita","year":"2018","journal-title":"Expert Rev Proteomics"},{"key":"2025070701243308700_ref3","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1016\/j.ijbiomac.2018.06.083","article-title":"Quantitative proteomic analysis and antivenom study revealing that neurotoxic phospholipase A2 enzymes, the major toxin class of Russell's viper venom from southern India, shows the least immuno-recognition and neutralization by commercial polyvalent antivenom","volume":"118","author":"Kalita","year":"2018","journal-title":"Int J Biol Macromol"},{"key":"2025070701243308700_ref4","doi-asserted-by":"publisher","first-page":"103443","DOI":"10.1016\/j.jprot.2019.103443","article-title":"Phylovenomics of Daboia russelii across the Indian subcontinent. Bioactivities and comparative in vivo neutralization and in vitro third-generation antivenomics of antivenoms against venoms from India, Bangladesh and Sri Lanka","volume":"207","author":"Pla","year":"2019","journal-title":"J Proteomics"},{"key":"2025070701243308700_ref5","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/0041-0101(89)90136-0","article-title":"Purification and characterization of a major phospholipase A2 from Russell's viper (Vipera russelli) venom","volume":"27","author":"Kasturi","year":"1989","journal-title":"Toxicon."},{"key":"2025070701243308700_ref6","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/S0041-0101(99)00228-7","article-title":"Molecular mechanism of lung hemorrhage induction by VRV-PL-VIIIa from Russell's viper (Vipera russelli) venom","volume":"38","author":"Uma","year":"2000","journal-title":"Toxicon"},{"key":"2025070701243308700_ref7","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1023\/A:1016591318855","article-title":"Purification and characterization of a potent hemolytic toxin with phospholipase A2 activity from the venom of Indian Russell's viper","volume":"237","author":"Chakraborty","year":"2002","journal-title":"Mol Cell Biochem"},{"key":"2025070701243308700_ref8","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/s12640-016-9650-4","article-title":"Neurotoxicity in Sri Lankan Russell's viper (Daboia russelii) envenoming is primarily due to U1-viperitoxin-Dr1a, a pre-synaptic neurotoxin","volume":"31","author":"Silva","year":"2017","journal-title":"Neurotox Res"},{"key":"2025070701243308700_ref9","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.toxicon.2020.07.011","article-title":"Sodium oleate, arachidonate, and linoleate enhance fibrinogenolysis by Russell's viper venom proteinases and inhibit FXIIIa; a role for phospholipase A2 in venom induced consumption coagulopathy","volume":"186","author":"Alangode","year":"2020","journal-title":"Toxicon"},{"key":"2025070701243308700_ref10","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/j.biochi.2013.11.026","article-title":"A major phospholipase A2 from Daboia russelii russelii venom shows potent anticoagulant action vi thrombin inhibition and binding with plasma phospholipids","volume":"99","author":"Mukherjee","year":"2014","journal-title":"Biochimie"},{"key":"2025070701243308700_ref11","doi-asserted-by":"publisher","first-page":"e0153770","DOI":"10.1371\/journal.pone.0153770","article-title":"Daboxin P, a major phospholipase A2 enzyme from the Indian Daboia russelii russelii venom targets factor X and factor Xa for its anticoagulant activity","volume":"11","author":"Sharma","year":"2016","journal-title":"PloS One"},{"key":"2025070701243308700_ref12","doi-asserted-by":"publisher","first-page":"e23476","DOI":"10.1002\/jbt.23476","article-title":"Daboxin P, a phospholipase a(2) of Indian Daboia russelii venom, modulates thrombin-mediated platelet aggregation","volume":"37","author":"Yasmin","year":"2023","journal-title":"J Biochem Mol Toxicol"},{"key":"2025070701243308700_ref13","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1016\/S0958-1669(00)00152-X","article-title":"Phage display in pharmaceutical biotechnology","volume":"11","author":"Sidhu","year":"2000","journal-title":"Curr Opin Biotechnol"},{"key":"2025070701243308700_ref14","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/0076-6879(93)17065-D","article-title":"Libraries of peptides and proteins displayed on filamentous phage","volume":"217","author":"Smith","year":"1993","journal-title":"Methods Enzymol"},{"key":"2025070701243308700_ref15","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1126\/science.1696028","article-title":"Searching for peptide ligands with an epitope library","volume":"249","author":"Scott","year":"1990","journal-title":"Science"},{"key":"2025070701243308700_ref16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/abio.1996.0241","article-title":"Filamentous phage display of oligopeptide libraries","volume":"238","author":"Burritt","year":"1996","journal-title":"Anal Biochem"},{"key":"2025070701243308700_ref17","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.bbapap.2005.07.020","article-title":"Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic acid at 1.8 a resolution","volume":"1752","author":"Balasubramanya","year":"2005","journal-title":"Biochim Biophys Acta"},{"key":"2025070701243308700_ref18","doi-asserted-by":"publisher","first-page":"2851","DOI":"10.1007\/s00018-009-0050-2","article-title":"Protein complexes in snake venom","volume":"66","author":"Doley","year":"2009","journal-title":"Cell Mol Life Sci"},{"key":"2025070701243308700_ref19","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1002\/pmic.200300680","article-title":"RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites","volume":"4","author":"Mandava","year":"2004","journal-title":"Proteomics"},{"key":"2025070701243308700_ref20","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.jmb.2005.12.039","article-title":"Phage display reveals multiple contact sites between FhuA, an outer membrane receptor of Escherichia coli, and TonB","volume":"357","author":"Carter","year":"2006","journal-title":"J Mol Biol"},{"key":"2025070701243308700_ref21","doi-asserted-by":"publisher","first-page":"9604","DOI":"10.1021\/bi000395z","article-title":"Recombinant antitoxic and antiinflammatory factor from the nonvenomous snake Python reticulatus: phospholipase A2 inhibition and venom neutralizing potential","volume":"39","author":"Thwin","year":"2000","journal-title":"Biochemistry"},{"key":"2025070701243308700_ref22","doi-asserted-by":"publisher","first-page":"15646","DOI":"10.1016\/S0021-9258(17)40730-7","article-title":"A phospholipase A2 inhibitor from the plasma of the south American rattlesnake (Crotalus durissus terrificus). Protein structure, genomic structure, and mechanism of action","volume":"269","author":"Fortes-Dias","year":"1994","journal-title":"J Biol Chem"},{"key":"2025070701243308700_ref23","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100014","article-title":"Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations","volume":"1","author":"Zheng","year":"2021","journal-title":"Cell Rep Methods"},{"key":"2025070701243308700_ref24","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER suite: protein structure and function prediction","volume":"12","author":"Yang","year":"2015","journal-title":"Nat Methods"},{"key":"2025070701243308700_ref25","doi-asserted-by":"publisher","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025070701243308700_ref26","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1038\/s41596-020-0312-x","article-title":"The HDOCK server for integrated protein-protein docking","volume":"15","author":"Yan","year":"2020","journal-title":"Nat Protoc"},{"key":"2025070701243308700_ref27","doi-asserted-by":"publisher","first-page":"W365","DOI":"10.1093\/nar\/gkx407","article-title":"HDOCK: a web server for protein-protein and protein-DNA\/RNA docking based on a hybrid strategy","volume":"45","author":"Yan","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025070701243308700_ref28","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1002\/pro.3235","article-title":"UCSF ChimeraX: meeting modern challenges in visualization and analysis","volume":"27","author":"Goddard","year":"2018","journal-title":"Protein Sci"},{"key":"2025070701243308700_ref29","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci"},{"key":"2025070701243308700_ref30","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/0378-1119(95)00058-E","article-title":"Characterization of phage that bind plastic from phage-displayed random peptide libraries","volume":"156","author":"Adey","year":"1995","journal-title":"Gene"},{"key":"2025070701243308700_ref31","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.ab.2004.09.048","article-title":"The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies","volume":"336","author":"Menendez","year":"2005","journal-title":"Anal Biochem"},{"key":"2025070701243308700_ref32","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1016\/S0022-2836(02)00844-6","article-title":"Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries","volume":"322","author":"Rodi","year":"2002","journal-title":"J Mol Biol"},{"key":"2025070701243308700_ref33","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1046\/j.0014-2956.2001.02711.x","article-title":"Functional site of endogenous phospholipase A2 inhibitor from python serum","volume":"269","author":"Thwin","year":"2002","journal-title":"Eur J Biochem"},{"key":"2025070701243308700_ref34","doi-asserted-by":"publisher","first-page":"5938","DOI":"10.1021\/jm070385x","article-title":"Novel peptide inhibitors of human secretory phospholipase A2 with antiinflammatory activity: solution structure and molecular modeling","volume":"50","author":"Thwin","year":"2007","journal-title":"J Med Chem"},{"key":"2025070701243308700_ref35","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1006\/bbrc.1995.2084","article-title":"A hypothetical structural role for proline residues in the flanking segments of protein-protein interaction sites","volume":"212","author":"Kini","year":"1995","journal-title":"Biochem Biophys Res Commun"},{"key":"2025070701243308700_ref36","doi-asserted-by":"publisher","first-page":"2852","DOI":"10.1002\/anie.200400618","article-title":"Recognition of proline-rich motifs by protein-protein-interaction domains","volume":"44","author":"Ball","year":"2005","journal-title":"Angew Chem Int Ed Engl"},{"key":"2025070701243308700_ref37","doi-asserted-by":"publisher","first-page":"107267","DOI":"10.1016\/j.toxicon.2023.107267","article-title":"Mapping possible interaction sites for crotoxin in CNF, a gamma PLA(2) inhibitor from Crotalus durissus terrificus rattle snake, using SPOT synthesis","volume":"234","author":"Campos","year":"2023","journal-title":"Toxicon"},{"key":"2025070701243308700_ref38","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1016\/j.bbapap.2014.05.001","article-title":"Insights on the structure of native CNF, an endogenous phospholipase A2 inhibitor from Crotalus durissus terrificus, the south American rattlesnake","volume":"1844","author":"Fortes-Dias","year":"2014","journal-title":"Biochim Biophys Acta"},{"key":"2025070701243308700_ref39","doi-asserted-by":"publisher","first-page":"3020","DOI":"10.1002\/1873-3468.13875","article-title":"Crystal structure of TEX101, a glycoprotein essential for male fertility, reveals the presence of tandemly arranged Ly6\/uPAR domains","volume":"594","author":"Masutani","year":"2020","journal-title":"FEBS Lett"},{"key":"2025070701243308700_ref40","doi-asserted-by":"publisher","DOI":"10.3390\/toxins8050155","article-title":"ADAM and ADAMTS family proteins and snake venom metalloproteinases: a structural overview","volume":"8","author":"Takeda","year":"2016","journal-title":"Toxins (Basel)"},{"key":"2025070701243308700_ref41","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1002\/pro.2230","article-title":"Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area","volume":"22","author":"Chen","year":"2013","journal-title":"Protein Sci"},{"key":"2025070701243308700_ref42","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1007\/s00221-003-1476-7","article-title":"Secretory phospholipase A2 activity in the normal and kainate injected rat brain, and inhibition by a peptide derived from python serum","volume":"150","author":"Thwin","year":"2003","journal-title":"Exp Brain Res"},{"key":"2025070701243308700_ref43","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.toxicon.2008.04.167","article-title":"Prospection, structural analysis and phylogenetic relationships of endogenous gamma-phospholipase a(2) inhibitors in Brazilian Bothrops snakes (Viperidae, Crotalinae)","volume":"52","author":"Estevao-Costa","year":"2008","journal-title":"Toxicon"},{"key":"2025070701243308700_ref44","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1016\/j.toxicon.2009.12.023","article-title":"Venom neutralization by purified bioactive molecules: synthetic peptide derivatives of the endogenous PLA(2) inhibitory protein PIP (a mini-review)","volume":"56","author":"Thwin","year":"2010","journal-title":"Toxicon"},{"key":"2025070701243308700_ref45","doi-asserted-by":"publisher","first-page":"6451","DOI":"10.1021\/bi8000962","article-title":"Interaction of group IA phospholipase A2 with metal ions and phospholipid vesicles probed with deuterium exchange mass spectrometry","volume":"47","author":"Burke","year":"2008","journal-title":"Biochemistry"}],"container-title":["Integrative Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ib\/article-pdf\/doi\/10.1093\/intbio\/zyaf012\/63679155\/zyaf012.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ib\/article-pdf\/doi\/10.1093\/intbio\/zyaf012\/63679155\/zyaf012.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T05:24:37Z","timestamp":1751865877000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ib\/article\/doi\/10.1093\/intbio\/zyaf012\/8188247"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":45,"URL":"https:\/\/doi.org\/10.1093\/intbio\/zyaf012","relation":{},"ISSN":["1757-9708"],"issn-type":[{"value":"1757-9708","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"zyaf012"}}