Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity
Identifieur interne : 000502 ( Main/Exploration ); précédent : 000501; suivant : 000503Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity
Auteurs : Richa Tambi ; Gentaro Morimoto ; Satoshi Kosuda ; Makoto Taiji ; Yutaka KurodaSource :
- Scientific Reports [ 2045-2322 ] ; 2019.
Abstract
In order to investigate the early phase of the amyloid formation by the short amyloidogenic octapeptide sequence (‘NFGAILSS’) derived from IAPP, we carried out a 100ns all-atom molecular dynamics (MD) simulations of systems that contain 27 peptides and over 30,000 water molecules. The large-scale calculations were performed for the wild type sequence and seven alanine-scanned sequences using AMBER 8.0 on RIKEN’s special purpose MD-GRAPE3 supercomputer, using the all-atom point charge force field ff99, which do not favor β-structures. Large peptide clusters (size 18–26 mers) were observed for all simulations, and our calculations indicated that isoleucine at position 5 played important role in the formation of β-rich clusters. In the oligomeric state, the wild type and the S7A sequences had the highest β-structure content (~14%), as calculated by DSSP, in line with experimental observations, whereas I5A and G3A had the highest helical content (~20%). Importantly, the β-structure preferences of wild type IAPP originate from its association into clusters and are not intrinsic to its sequence. Altogether, the results of this first large-scale, multi-peptide all-atom molecular dynamics simulation appear to provide insights into the mechanism of amyloidogenic and non-amyloidogenic oligomers that mainly corroborate previous experimental observations.
Url:
DOI: 10.1038/s41598-018-38401-w
PubMed: 30792475
PubMed Central: 6384915
Affiliations:
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Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3">Present Address: College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, 505055 UAE</nlm:aff><wicri:noCountry code="subfield">505055 UAE</wicri:noCountry></affiliation></author><author><name sortKey="Morimoto, Gentaro" sort="Morimoto, Gentaro" uniqKey="Morimoto G" first="Gentaro" last="Morimoto">Gentaro Morimoto</name><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000000094465255</institution-id><institution-id institution-id-type="GRID">grid.7597.c</institution-id><institution>Computational Biology Research Core,</institution><institution>Quantitative Biology Center (QBiC), RIKEN, 6-2-3, Furuedai,</institution></institution-wrap>Suita, Osaka 565-0874 Japan</nlm:aff><wicri:noCountry code="subfield">Osaka 565-0874 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Kosuda, Satoshi" sort="Kosuda, Satoshi" uniqKey="Kosuda S" first="Satoshi" last="Kosuda">Satoshi Kosuda</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.136594.c</institution-id><institution>Department of Biotechnology and Life Sciences, Graduate School of Engineering,</institution><institution>Tokyo University of Agriculture and Technology,</institution></institution-wrap>2-24-16, Nakamachi, Koganei, Tokyo 184-8588 Japan</nlm:aff><wicri:noCountry code="subfield">Tokyo 184-8588 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Taiji, Makoto" sort="Taiji, Makoto" uniqKey="Taiji M" first="Makoto" last="Taiji">Makoto Taiji</name><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000000094465255</institution-id><institution-id institution-id-type="GRID">grid.7597.c</institution-id><institution>Computational Biology Research Core,</institution><institution>Quantitative Biology Center (QBiC), RIKEN, 6-2-3, Furuedai,</institution></institution-wrap>Suita, Osaka 565-0874 Japan</nlm:aff><wicri:noCountry code="subfield">Osaka 565-0874 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Kuroda, Yutaka" sort="Kuroda, Yutaka" uniqKey="Kuroda Y" first="Yutaka" last="Kuroda">Yutaka Kuroda</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.136594.c</institution-id><institution>Department of Biotechnology and Life Sciences, Graduate School of Engineering,</institution><institution>Tokyo University of Agriculture and Technology,</institution></institution-wrap>2-24-16, Nakamachi, Koganei, Tokyo 184-8588 Japan</nlm:aff><wicri:noCountry code="subfield">Tokyo 184-8588 Japan</wicri:noCountry></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="Par1">In order to investigate the early phase of the amyloid formation by the short amyloidogenic octapeptide sequence (‘NFGAILSS’) derived from IAPP, we carried out a 100ns all-atom molecular dynamics (MD) simulations of systems that contain 27 peptides and over 30,000 water molecules. The large-scale calculations were performed for the wild type sequence and seven alanine-scanned sequences using AMBER 8.0 on RIKEN’s special purpose MD-GRAPE3 supercomputer, using the all-atom point charge force field ff99, which do not favor β-structures. Large peptide clusters (size 18–26 mers) were observed for all simulations, and our calculations indicated that isoleucine at position 5 played important role in the formation of β-rich clusters. In the oligomeric state, the wild type and the S7A sequences had the highest β-structure content (~14%), as calculated by DSSP, in line with experimental observations, whereas I5A and G3A had the highest helical content (~20%). Importantly, the β-structure preferences of wild type IAPP originate from its association into clusters and are not intrinsic to its sequence. Altogether, the results of this first large-scale, multi-peptide all-atom molecular dynamics simulation appear to provide insights into the mechanism of amyloidogenic and non-amyloidogenic oligomers that mainly corroborate previous experimental observations.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Eisenberg, D" uniqKey="Eisenberg D">D Eisenberg</name></author><author><name sortKey="Jucker, M" uniqKey="Jucker M">M Jucker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goto, Y" uniqKey="Goto Y">Y Goto</name></author><author><name sortKey="Yagi, H" uniqKey="Yagi H">H Yagi</name></author><author><name sortKey="Yamaguchi, K" uniqKey="Yamaguchi K">K Yamaguchi</name></author><author><name sortKey="Chatani, E" uniqKey="Chatani E">E Chatani</name></author><author><name sortKey="Ban, T" uniqKey="Ban T">T Ban</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hall, 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Kabsch</name></author><author><name sortKey="Sander, C" uniqKey="Sander C">C Sander</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcdonald, Ik" uniqKey="Mcdonald I">IK McDonald</name></author><author><name sortKey="Thornton, Jm" uniqKey="Thornton J">JM Thornton</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Kosuda, Satoshi" sort="Kosuda, Satoshi" uniqKey="Kosuda S" first="Satoshi" last="Kosuda">Satoshi Kosuda</name><name sortKey="Kuroda, Yutaka" sort="Kuroda, Yutaka" uniqKey="Kuroda Y" first="Yutaka" last="Kuroda">Yutaka Kuroda</name><name sortKey="Morimoto, Gentaro" sort="Morimoto, Gentaro" uniqKey="Morimoto G" first="Gentaro" last="Morimoto">Gentaro Morimoto</name><name sortKey="Taiji, Makoto" sort="Taiji, Makoto" uniqKey="Taiji M" first="Makoto" last="Taiji">Makoto Taiji</name><name sortKey="Tambi, Richa" sort="Tambi, Richa" uniqKey="Tambi R" first="Richa" 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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:30792475" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |