{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:06:04Z","timestamp":1789477564438,"version":"build-2803163510"},"reference-count":49,"publisher":"American Chemical Society (ACS)","issue":"18","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100008605","name":"Indian National Science Academy","doi-asserted-by":"publisher","award":["INSA\/SP\/HS \/2024\/ dated 24-07-2024"],"award-info":[{"award-number":["INSA\/SP\/HS \/2024\/ dated 24-07-2024"]}],"id":[{"id":"10.13039\/100008605","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR40174\/BTIS\/137\/45\/2022"],"award-info":[{"award-number":["BT\/PR40174\/BTIS\/137\/45\/2022"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["DST\/WIDUSHI-B\/LS\/2023\/20"],"award-info":[{"award-number":["DST\/WIDUSHI-B\/LS\/2023\/20"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001502","name":"Department of Atomic Energy, Government of India","doi-asserted-by":"publisher","award":["1003\/11\/2021\/RRF\/R&D-II\/9855"],"award-info":[{"award-number":["1003\/11\/2021\/RRF\/R&D-II\/9855"]}],"id":[{"id":"10.13039\/501100001502","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>To understand the differences resulting from the presence of an \u03b1- or \u03b2-amino acid in a peptide, we used two sets of amino acids corresponding to Asp\/isoAsp and Ala\/isoAla in two types of host peptides: one containing Gly (with no side chains) and the other containing Ala (representing amino acids with side chains), and measured their tendency to form fibrils. The peptides with a \u03b2-amino acid formed fibrils, while those with an \u03b1-amino acid did not exhibit this proclivity, as inferred from the thioflavin T (ThT) fluorescence intensity measurements. The fibrillation of the hexapeptide with isoAsp (the \u03b2-amino acid corresponding to Asp) was inhibited by protein-l-isoaspartyl methyltransferase (PIMT), a repair enzyme that converts the abnormal isoAsp residue to normal Asp. Isothermal Titration Calorimetry revealed the exothermic mode of binding of A6-isoAsp (Ala-based host hexapeptide) with PIMT. Far-UV CD spectroscopy revealed a \u03b2-sheet to \u03b1-helix transformation of isoAsp-containing peptides in the presence of PIMT. The hydrophobicity of the peptides was measured by noting their distribution in a mixture of water and octanol, where the \u03b2-amino acid exhibits a more positive hydrophobicity value than the \u03b1-amino acid. This may suggest that the hydrophobic forces bring chains containing \u03b2-amino acids together to enable nucleation for fibril formation. Molecular dynamics (MD) simulations indicated that isoAsp-based host peptides, formed into fibrils, have stable structures over the course of simulations, whereas the equivalent peptide with Asp disintegrated. Models of a single \u03b2-strand of these peptides bound to the active site of the enzyme were stable.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00401","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T02:55:25Z","timestamp":1788317725000},"page":"2885-2895","source":"Crossref","is-referenced-by-count":0,"title":["Factors Influencing\nthe Selection of \u03b1-Amino\nAcids over \u03b2-Amino Acids in Nature: Studies Involving\nProtein-\n                    <scp>l<\/scp>\n                    -isoaspartyl Methyltransferase Substrates\nand Related Peptides"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1894-5099","authenticated-orcid":true,"given":"Tanaya","family":"Chatterjee","sequence":"first","affiliation":[{"name":"Bose Institute , , EN Block Sector V , ,","place":["Kolkata, India, 700091"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debarati","family":"Paul","sequence":"additional","affiliation":[{"name":"Bose Institute , , EN Block Sector V , ,","place":["Kolkata, India, 700091"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0692-8139","authenticated-orcid":true,"given":"Shubhra","family":"Ghosh Dastidar","sequence":"additional","affiliation":[{"name":"Bose Institute , , EN Block Sector V , ,","place":["Kolkata, India, 700091"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pinak","family":"Chakrabarti","sequence":"additional","affiliation":[{"name":"Bose Institute , EN Block Sector V , ,","place":["Kolkata, India, 700091"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"issue":"1","key":"2026091508070612300_cit1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-35795-8","article-title":"Control of Protein\nStability by Post-Translational Modifications","volume":"14","author":"Lee","year":"2023","journal-title":"Nat. Commun."},{"issue":"3","key":"2026091508070612300_cit2","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1039\/b111145k","article-title":"Nonribosomal Peptides:\nFrom Genes\nto Products","volume":"20","author":"Schwarzer","year":"2003","journal-title":"Nat. Prod. Rep."},{"issue":"8","key":"2026091508070612300_cit3","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1002\/cbdv.200490087","article-title":"The World\nof Beta- and Gamma-Peptides\nComprised of Homologated Proteinogenic Amino Acids and Other Components","volume":"1","author":"Seebach","year":"2004","journal-title":"Chem. Biodiversity"},{"issue":"10","key":"2026091508070612300_cit4","doi-asserted-by":"publisher","first-page":"3219","DOI":"10.1021\/cr000045i","article-title":"Beta-Peptides:\nFrom Structure to\nFunction","volume":"101","author":"Cheng","year":"2001","journal-title":"Chem. Rev."},{"issue":"23","key":"2026091508070612300_cit5","doi-asserted-by":"publisher","first-page":"9718","DOI":"10.1021\/jm5010896","article-title":"Peptides Containing\n\u03b2-Amino Acid Patterns: Challenges and Successes in Medicinal\nChemistry","volume":"57","author":"Cabrele","year":"2014","journal-title":"J. Med. Chem."},{"issue":"2","key":"2026091508070612300_cit6","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/S0021-9258(19)75855-4","article-title":"Deamidation, Isomerization,\nand Racemization at Asparaginyl\nand Aspartyl Residues in Peptides. Succinimide-Linked Reactions That\nContribute to Protein Degradation","volume":"262","author":"Geiger","year":"1987","journal-title":"J. Biol.\nChem."},{"issue":"12","key":"2026091508070612300_cit7","doi-asserted-by":"publisher","first-page":"5622","DOI":"10.1016\/S0021-9258(18)45619-0","article-title":"Protein\nCarboxyl Methyltransferase Facilitates Conversion of Atypical L-Isoaspartyl\nPeptides to Normal L-Aspartyl Peptides","volume":"262","author":"Johnson","year":"1987","journal-title":"J. Biol.\nChem."},{"issue":"9","key":"2026091508070612300_cit8","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1248\/bpb.28.1590","article-title":"Biological\nSignificance of Isoaspartate\nand Its Repair System","volume":"28","author":"Shimizu","year":"2005","journal-title":"Biol. Pharm. Bull."},{"issue":"3","key":"2026091508070612300_cit9","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagen.2019.129500","article-title":"The Role of\nIsoaspartate in Fibrillation and Its Prevention\nby Protein-L-Isoaspartyl Methyltransferase","volume":"1864","author":"Chatterjee","year":"2020","journal-title":"Biochim. Biophys. 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Rev."},{"issue":"1","key":"2026091508070612300_cit23","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.102801","article-title":"Intrinsically Disordered\nRegions That Drive Phase Separation Form a Robustly Distinct Protein\nClass","volume":"299","author":"Ibrahim","year":"2023","journal-title":"J. Biol. Chem."},{"key":"2026091508070612300_cit24","first-page":"369","article-title":"Hydrophobic Parameters\nII of Amino Acid Side-Chains\nfrom the Partitioning of N-Acetyl-Amino Acid Amides","volume":"18","author":"Fauchere","year":"1983","journal-title":"Eur. J. Med. 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Educ."},{"key":"2026091508070612300_cit31","unstructured":"PyMOL\n| pymol.org. https:\/\/www.pymol.org\/ (accessed Feb 26, 2026)."},{"issue":"11","key":"2026091508070612300_cit32","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A Web-Based Graphical\nUser Interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"issue":"1","key":"2026091508070612300_cit33","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m:\nAn Improved Force Field for Folded and Intrinsically Disordered Proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nat. 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Drug Discovery"},{"issue":"2","key":"2026091508070612300_cit43","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1016\/j.bbagen.2014.10.022","article-title":"Antibacterial\nEffect of Silver Nanoparticles and the Modeling of Bacterial Growth\nKinetics Using a Modified Gompertz Model","volume":"1850","author":"Chatterjee","year":"2015","journal-title":"Biochim.\nBiophys. Acta, Gen. Subj."},{"issue":"28","key":"2026091508070612300_cit44","doi-asserted-by":"publisher","first-page":"30256","DOI":"10.1021\/acsomega.4c00500","article-title":"Inhibition of the Early-Stage Cross-Amyloid\nAggregation\nof Amyloid-\u03b2 and IAPP via EGCG: Insights from Molecular Dynamics\nSimulations","volume":"9","author":"Srivastava","year":"2024","journal-title":"ACS Omega"},{"issue":"1","key":"2026091508070612300_cit45","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual\nMolecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graphics"},{"key":"2026091508070612300_cit46","doi-asserted-by":"crossref","unstructured":"Gowers, R. J.; Linke, M.; Barnoud, J.; Reddy, T. J. E.; Melo, M. N.; Seyler, S. L.; Doman\u0301ski, J.; Dotson, D. L.; Buchoux, S.; Kenney, I. M.; Beckstein, O. 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Chem."},{"issue":"12","key":"2026091508070612300_cit48","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of Protein\nSecondary Structure: Pattern\nRecognition of Hydrogen-Bonded and Geometrical Features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"issue":"8","key":"2026091508070612300_cit49","doi-asserted-by":"publisher","DOI":"10.1002\/pro.70208","article-title":"DSSP 4: FAIR Annotation\nof Protein Secondary Structure","volume":"34","author":"Hekkelman","year":"2025","journal-title":"Protein Sci."}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00401","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/18\/2885\/67592209\/acs.biochem.6c00401.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/18\/2885\/67592209\/acs.biochem.6c00401.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:22:56Z","timestamp":1789474976000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/18\/2885\/5348003\/Factors-Influencing-the-Selection-of-Amino-Acids"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,28]]},"references-count":49,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,8,28]]},"published-print":{"date-parts":[[2026,9,15]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00401","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,28]]}}}