Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations
Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protami...
Saved in:
| Published in: | ACS omega Vol. 7; no. 46; pp. 42083 - 42095 |
|---|---|
| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
American Chemical Society
22-11-2022
|
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protamine varied widely, indicating that they were disordered with structures covering a broad conformational landscape, from hairpin loop structures to extended coils. Despite their general disorder, the protamines did form secondary structures, including helices and hairpin loops. In eutherians, hairpins may promote disulfide bonding that facilitates protamine-DNA condensation, but the specifics of this bonding is not well established. We examined inter-residue distances in the simulations to predict residue pairs likely to form intramolecular bonds, leading to the identification of bonding pairs consistent with previous results in bull and human. These results support a model for eutherian protamine structures where a highly charged center is surrounded by disulfide-bond-stabilized loops. |
|---|---|
| AbstractList | Protamines are arginine-rich
proteins that condense DNA in sperm.
Despite their importance in reproduction, information on protamine
structure is scarce. We, therefore, used molecular dynamics to examine
the structures of salmon, bull P1, and human P1 protamines. The sizes
and shapes of each protamine varied widely, indicating that they were
disordered with structures covering a broad conformational landscape,
from hairpin loop structures to extended coils. Despite their general
disorder, the protamines did form secondary structures, including
helices and hairpin loops. In eutherians, hairpins may promote disulfide
bonding that facilitates protamine-DNA condensation, but the specifics
of this bonding is not well established. We examined inter-residue
distances in the simulations to predict residue pairs likely to form
intramolecular bonds, leading to the identification of bonding pairs
consistent with previous results in bull and human. These results
support a model for eutherian protamine structures where a highly
charged center is surrounded by disulfide-bond-stabilized loops. Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protamine varied widely, indicating that they were disordered with structures covering a broad conformational landscape, from hairpin loop structures to extended coils. Despite their general disorder, the protamines did form secondary structures, including helices and hairpin loops. In eutherians, hairpins may promote disulfide bonding that facilitates protamine-DNA condensation, but the specifics of this bonding is not well established. We examined inter-residue distances in the simulations to predict residue pairs likely to form intramolecular bonds, leading to the identification of bonding pairs consistent with previous results in bull and human. These results support a model for eutherian protamine structures where a highly charged center is surrounded by disulfide-bond-stabilized loops. |
| Author | Wang, Yongmei Ziebarth, Jesse D. DeRouchey, Jason E. Gallops, Caleb Edward Shadman, Hossain |
| AuthorAffiliation | Department of Chemistry |
| AuthorAffiliation_xml | – name: Department of Chemistry |
| Author_xml | – sequence: 1 givenname: Hossain orcidid: 0000-0002-4020-4783 surname: Shadman fullname: Shadman, Hossain organization: Department of Chemistry – sequence: 2 givenname: Caleb Edward surname: Gallops fullname: Gallops, Caleb Edward organization: Department of Chemistry – sequence: 3 givenname: Jesse D. surname: Ziebarth fullname: Ziebarth, Jesse D. organization: Department of Chemistry – sequence: 4 givenname: Jason E. orcidid: 0000-0002-3624-4432 surname: DeRouchey fullname: DeRouchey, Jason E. organization: Department of Chemistry – sequence: 5 givenname: Yongmei orcidid: 0000-0002-7418-9489 surname: Wang fullname: Wang, Yongmei email: ywang@memphis.edu organization: Department of Chemistry |
| BookMark | eNp1UctKAzEUDVLBWrt3OUsXtuYxM0k2gtT6gIpCdR3STGY6ZSapyUTs35vS1sdCuHBf55wL95yCnrFGA3CO4BhBjK6k8rbVlRxjBVOM6RHo45TCESIp6f2qT8DQ-xWEEOUMM5z3gZh-rhvralMl884F1QWnfSJNkdxujGxr5RNbJi_OdrExOnmyjVahiZhu6WyoloeJdD-Med3GQVdb48_AcSkbr4f7PABvd9PXycNo9nz_OLmZjWSKYDfiqMSaUo4pV-VCKU0zlS-YZLTgDGOZUY4yIhWRhGiOUYZZxjOCSFnGoAUZgOud7josWl0obTonG7F2dSvdRlhZi78bUy9FZT8Ez1lGGYkCF3sBZ9-D9p1oa69000ijbfAC0xRySFm2hcIdVDnrvdPl9xkExdYPcfBD7P2IlMsdJW7EygZn4jP-h38BKraTXQ |
| CitedBy_id | crossref_primary_10_1021_acs_biochem_3c00562 crossref_primary_10_1021_jacs_3c07846 crossref_primary_10_1016_j_bpj_2024_04_010 crossref_primary_10_1097_MD_0000000000036113 crossref_primary_10_1016_j_bpj_2023_10_003 |
| Cites_doi | 10.1002/bip.360221211 10.3390/cells9091994 10.1093/humupd/dml009 10.3390/ijms222011058 10.1016/j.bpj.2017.08.050 10.1016/S0079-6603(08)60839-9 10.1021/ct400314y 10.1093/nar/gkab354 10.1016/j.pbiomolbio.2015.03.003 10.3136/nskkk.55.360 10.1186/s12610-016-0044-5 10.1007/128_2011_171 10.1016/j.jsb.2018.03.011 10.1093/nar/gkaa1100 10.1021/acsomega.0c01867 10.1016/j.cpc.2012.09.022 10.1021/acs.jpcb.8b09029 10.1016/j.bbagrm.2013.08.004 10.1021/acsomega.9b00066 10.1038/s41586-021-03819-2 10.1063/1.470117 10.1016/0263-7855(96)00018-5 10.1021/bi00190a005 10.3389/fgene.2019.00962 10.1074/jbc.M312777200 10.1021/mz500681y 10.1021/acs.jcim.7b00135 10.1006/jmbi.1999.3091 10.1016/j.jmb.2021.167208 10.1101/gad.290916.116 10.1093/oxfordjournals.molbev.a026153 10.1186/gb-2007-8-9-227 10.1016/j.apjr.2016.07.013 10.1021/ma800212n 10.1021/bm900275s 10.2174/157340909789577865 10.1021/ct400341p 10.1021/ct200909j 10.1021/bi00215a026 10.1093/bioinformatics/btg224 10.1021/acs.jctc.5b00255 10.1126/science.286.5437.120 10.1074/jbc.M111.295808 10.5281/zenodo.44612 10.1007/BF01116555 10.1186/s12864-020-6681-2 10.1016/j.freeradbiomed.2014.07.037 10.1073/pnas.1907251116 10.1093/nar/gkab1061 10.1530/rep.0.1250625 10.1038/s41598-020-67230-z 10.1530/REP-09-0281 |
| ContentType | Journal Article |
| Copyright | 2022 The Authors. Published by American Chemical Society 2022 The Authors. Published by American Chemical Society 2022 The Authors |
| Copyright_xml | – notice: 2022 The Authors. Published by American Chemical Society – notice: 2022 The Authors. Published by American Chemical Society 2022 The Authors |
| DBID | N~. AAYXX CITATION 7X8 5PM |
| DOI | 10.1021/acsomega.2c04227 |
| DatabaseName | American Chemical Society (ACS) Open Access CrossRef MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE - Academic |
| DatabaseTitleList | |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Chemistry |
| EISSN | 2470-1343 |
| EndPage | 42095 |
| ExternalDocumentID | 10_1021_acsomega_2c04227 b65486837 |
| GrantInformation_xml | – fundername: ; grantid: MCB-1453168 |
| GroupedDBID | 53G ABFRP ABUCX ACS ADBBV AFEFF ALMA_UNASSIGNED_HOLDINGS AOIJS BCNDV EBS GROUPED_DOAJ HYE N~. OK1 RPM VF5 AAFWJ AAHBH AAYXX AFPKN CITATION M~E 7X8 5PM |
| ID | FETCH-LOGICAL-a410t-91f2e779279cfbcce75c6b8a87d9822a579153ac3a33e921528595313ff3ff7d3 |
| IEDL.DBID | RPM |
| ISSN | 2470-1343 |
| IngestDate | Tue Sep 17 21:31:50 EDT 2024 Sat Aug 17 03:08:20 EDT 2024 Fri Aug 23 01:21:56 EDT 2024 Thu Nov 24 04:02:03 EST 2022 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 46 |
| Language | English |
| License | Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a410t-91f2e779279cfbcce75c6b8a87d9822a579153ac3a33e921528595313ff3ff7d3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0002-7418-9489 0000-0002-4020-4783 0000-0002-3624-4432 |
| OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685783/ |
| PQID | 2740907853 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_9685783 proquest_miscellaneous_2740907853 crossref_primary_10_1021_acsomega_2c04227 acs_journals_10_1021_acsomega_2c04227 |
| PublicationCentury | 2000 |
| PublicationDate | 2022-11-22 |
| PublicationDateYYYYMMDD | 2022-11-22 |
| PublicationDate_xml | – month: 11 year: 2022 text: 2022-11-22 day: 22 |
| PublicationDecade | 2020 |
| PublicationTitle | ACS omega |
| PublicationTitleAlternate | ACS Omega |
| PublicationYear | 2022 |
| Publisher | American Chemical Society |
| Publisher_xml | – name: American Chemical Society |
| References | ref9/cit9 ref45/cit45 ref3/cit3 ref27/cit27 ref16/cit16 ref52/cit52 ref23/cit23 ref8/cit8 ref31/cit31 ref2/cit2 ref34/cit34 ref37/cit37 ref20/cit20 ref48/cit48 ref17/cit17 ref10/cit10 ref35/cit35 ref53/cit53 ref19/cit19 ref21/cit21 ref42/cit42 ref46/cit46 ref49/cit49 ref13/cit13 ref24/cit24 ref38/cit38 ref50/cit50 ref6/cit6 ref36/cit36 ref18/cit18 ref11/cit11 ref25/cit25 ref29/cit29 ref32/cit32 ref39/cit39 ref14/cit14 ref5/cit5 ref51/cit51 ref43/cit43 ref28/cit28 ref40/cit40 ref26/cit26 ref12/cit12 ref15/cit15 ref41/cit41 ref22/cit22 ref33/cit33 ref4/cit4 ref30/cit30 ref47/cit47 ref1/cit1 ref44/cit44 ref7/cit7 |
| References_xml | – ident: ref37/cit37 doi: 10.1002/bip.360221211 – ident: ref52/cit52 doi: 10.3390/cells9091994 – ident: ref3/cit3 doi: 10.1093/humupd/dml009 – ident: ref39/cit39 doi: 10.3390/ijms222011058 – ident: ref11/cit11 doi: 10.1016/j.bpj.2017.08.050 – ident: ref7/cit7 doi: 10.1016/S0079-6603(08)60839-9 – ident: ref32/cit32 doi: 10.1021/ct400314y – ident: ref47/cit47 doi: 10.1093/nar/gkab354 – ident: ref20/cit20 doi: 10.1016/j.pbiomolbio.2015.03.003 – ident: ref24/cit24 doi: 10.3136/nskkk.55.360 – ident: ref6/cit6 doi: 10.1186/s12610-016-0044-5 – ident: ref50/cit50 doi: 10.1007/128_2011_171 – ident: ref45/cit45 doi: 10.1016/j.jsb.2018.03.011 – ident: ref26/cit26 doi: 10.1093/nar/gkaa1100 – ident: ref42/cit42 doi: 10.1021/acsomega.0c01867 – ident: ref33/cit33 doi: 10.1016/j.cpc.2012.09.022 – ident: ref21/cit21 doi: 10.1021/acs.jpcb.8b09029 – ident: ref2/cit2 doi: 10.1016/j.bbagrm.2013.08.004 – ident: ref43/cit43 doi: 10.1021/acsomega.9b00066 – ident: ref48/cit48 doi: 10.1038/s41586-021-03819-2 – ident: ref30/cit30 doi: 10.1063/1.470117 – ident: ref35/cit35 doi: 10.1016/0263-7855(96)00018-5 – ident: ref25/cit25 doi: 10.1021/bi00190a005 – ident: ref9/cit9 doi: 10.3389/fgene.2019.00962 – ident: ref10/cit10 doi: 10.1074/jbc.M312777200 – ident: ref17/cit17 doi: 10.1021/mz500681y – ident: ref22/cit22 doi: 10.1021/acs.jcim.7b00135 – ident: ref46/cit46 doi: 10.1006/jmbi.1999.3091 – ident: ref53/cit53 doi: 10.1016/j.jmb.2021.167208 – ident: ref16/cit16 doi: 10.1101/gad.290916.116 – ident: ref5/cit5 doi: 10.1093/oxfordjournals.molbev.a026153 – ident: ref1/cit1 doi: 10.1186/gb-2007-8-9-227 – ident: ref8/cit8 doi: 10.1016/j.apjr.2016.07.013 – ident: ref38/cit38 doi: 10.1021/ma800212n – ident: ref14/cit14 doi: 10.1021/bm900275s – ident: ref44/cit44 doi: 10.2174/157340909789577865 – ident: ref34/cit34 doi: 10.1021/ct400341p – ident: ref31/cit31 doi: 10.1021/ct200909j – ident: ref15/cit15 doi: 10.1021/bi00215a026 – ident: ref41/cit41 doi: 10.1093/bioinformatics/btg224 – ident: ref29/cit29 doi: 10.1021/acs.jctc.5b00255 – ident: ref28/cit28 – ident: ref12/cit12 doi: 10.1126/science.286.5437.120 – ident: ref23/cit23 doi: 10.1074/jbc.M111.295808 – ident: ref36/cit36 doi: 10.5281/zenodo.44612 – ident: ref27/cit27 doi: 10.1007/BF01116555 – ident: ref18/cit18 doi: 10.1186/s12864-020-6681-2 – ident: ref51/cit51 doi: 10.1016/j.freeradbiomed.2014.07.037 – ident: ref19/cit19 doi: 10.1073/pnas.1907251116 – ident: ref49/cit49 doi: 10.1093/nar/gkab1061 – ident: ref4/cit4 doi: 10.1530/rep.0.1250625 – ident: ref40/cit40 doi: 10.1038/s41598-020-67230-z – ident: ref13/cit13 doi: 10.1530/REP-09-0281 |
| SSID | ssj0001682826 |
| Score | 2.3014386 |
| Snippet | Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We,... Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We,... |
| SourceID | pubmedcentral proquest crossref acs |
| SourceType | Open Access Repository Aggregation Database Publisher |
| StartPage | 42083 |
| SummonAdditionalLinks | – databaseName: American Chemical Society Journals dbid: ACS link: http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV05T8MwFLagDLBwI8olI8HAYEjsJnbGqoe6gJACEpvlODZ0aIKa9v_znKMHQgikLHEcy3rPeUee_X0I3Ti8l9R6jBiVpAT8sSUioJroJEwTj1PjcXd2eBTzpzfRH6zC5Hyv4FP_Qekin5h3dU-1w6vim2iLck-4RKvbi5f_U0LIHUp2NdrhHvFZh9VVyZ8Gcb5IF-u-aBlgrm-PXPE3w73_zHQf7dZRJe5Wy-AAbZjsEG33GjK3IyQXe-1wXCLGziHNxipLcb-ipC9wbvHzNJ_BTWbwY8WaC31qIp-mRU2Xb8TjSU3-VRyj1-HgpTciNbcCUR3fm4GNs9RwHlEeaZtobXigw0Qo0JxD9FMBj8AWKs0UYyZy5LcOCI35zFq4eMpOUCvLM3OKsMegiXERpmU4ZoXSiaGBENb4gRJJG92CZGT9bRSyLHtTXzbikrW42uiu0Yb8rKA2ful73ahLgiRdkUNlJp8XErJsDxJ-iELaiK_pcTGoQ9Ref5KNP0pk7SgUYMHY2R9nfI52qDsN4fuE0gvUAv2ZS7RZpPOrcnF-AXYw5FM priority: 102 providerName: American Chemical Society |
| Title | Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations |
| URI | http://dx.doi.org/10.1021/acsomega.2c04227 https://search.proquest.com/docview/2740907853 https://pubmed.ncbi.nlm.nih.gov/PMC9685783 |
| Volume | 7 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV07b4MwELaaLO1S9ammj4hK7dCBAHbBZqxooiypItFK3ZAxdhupQBSS_9-zgSQsHSqxYGyE7k6-O-78fQg9aLyXTLnEljzNbPDHymY-FrZIgyx1KZYu1WeHpzF9-2SvYw2T47dnYUzTvkgXo-InHxWLb9NbucyF0_aJOfNZFAYMDI04PdSD2HAvRTc_VgJIInBbkgQX5nBRlbn84iMsNOKVcUSi6jqiXXTZ7Y3cczaTE3TcRInWS_01p-hAFmfoMGrJ2c5Rsu2ds2KDALuBtNniRWa91hTzlVUqa74q13BTSGtWs-DCnIaYpx3hq92KeJE3ZF7VBfqYjN-jqd1wJdj82XPXsGcpLCkNMQ2FSoWQ1BdByjhoQiP0cZ-GsLdxQTghMtRkthrYjHhEKbhoRi5RvygLeYUsl8AQoSzITHilGBepxD5jSno-Z-kAPYL4ksbWq8SUsbGXtGJOGjEP0FMr4GRZQ2f8Mfe-1UACktRFC17IclMlkDW7kMBDVDFAtKOa7Us1Qnb3CRiOQcpuDOX63ytv0BHW5x08z8b4FvVBo_IO9apsM4QoPIqHJocfGgv8BbWP5WM |
| link.rule.ids | 230,315,729,782,786,866,887,2771,27087,27935,27936,53803,53805,56750,56800 |
| linkProvider | National Library of Medicine |
| linkToHtml | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV07T8MwED7xGGDhjSjPIMHAkDaxSeyMqC0qgqJKLRKb5Tg2VKIJIvT_c3YTaBeGSlkS21Hkz_bdxefvA7iyfC-ZCaivZZr5aI-NzyOifJXGWRowogNmzw73huz5lXe6liYnqs_CuKR9lY6b-cekmY_fXW7l50S16jyx1qDfTmKOA422VmEd52tA54J092slxjCC1JuSaMRaUpXFRL_JJlGW88qZIlUumqI__3IxO3LO3NxvL_mhO7BV-Zfe3ax4F1Z0vgcb7VrWbR_Eb9adN3TcsVMMuD2ZZ15nJk5feoXxBl_FN97k2uvP9HOxTiXpUz-RX38thuNJJQNWHsDLfXfU7vmVyoIvb8PgG1c7QzRjCWGJMqlSmkUqTrlEDC23n4xYgquiVFRSqhMrg2sp0WhIjcGLZfQQ1vIi10fgBRQfUcbjzDlmhkuVahJxbnQYSZ424Bq7XVSzpBRuA5yEooZHVPA04KYGRnzOSDf-qXtZIyewJ-12h8x1MS0FxtsBhv7ojzSALUD6-1LLrb1Ygkg6ju0KueOlW17ARm_UfxJPD8-PJ7BJ7KmJMPQJOYU1RFefwWqZTc_dyP0BimH5Dw |
| linkToPdf | http://sdu.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3LTuswEB3xkIANjwuI8gzSZcEiTWKT2Fmilgp0L6hSQWJnOY4NlWhSNfT_GbtJoRsWIGUTx44iH9szE4_PAfhr-V5yE1Jfyyz30R4bn8dE-SpL8ixkRIfMnh2-HbCHZ969sTQ5c6kvl7SvsmG7eBu1i-Gry60cj1TQ5IkF_ftOmnAcaDQY5yZYhlWcs2H8JVB3v1cSDCVIszGJhiyQqipH-kW2ibK8V84cqWrRHH36mIsZkl9MTm_rFx-7DZu1n-ldz6rswJIu_sB6p5F32wUxz77zBo5DdoqBtyeL3OvOROorrzRef1K-402hvfuZji7WqaV9mhI5-WwxGI5qObBqD556N4-dW79WW_DlVRS-46pniGYsJSxVJlNKs1glGZeIpeX4kzFLcXWUikpKdWrlcC01Go2oMXixnO7DSlEW-gC8kGIRZTzJnYNmuFSZJjHnRkex5FkLLrDrRT1bKuE2wkkkGohEDVELLhtwxHhGvvFN3fMGPYE9abc9ZKHLaSUw7g5T9IRi2gK2AOv8pZZje_EJoum4tmv0Dn_c8gzW-t2e-H_38O8INog9PBFFPiHHsILg6hNYrvLpqRu8H0cy-48 |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Exploring+Structures+and+Dynamics+of+Protamine+Molecules+through+Molecular+Dynamics+Simulations&rft.jtitle=ACS+omega&rft.au=Shadman%2C+Hossain&rft.au=Gallops%2C+Caleb+Edward&rft.au=Ziebarth%2C+Jesse+D&rft.au=DeRouchey%2C+Jason+E&rft.date=2022-11-22&rft.eissn=2470-1343&rft.volume=7&rft.issue=46&rft.spage=42083&rft.epage=42095&rft_id=info:doi/10.1021%2Facsomega.2c04227&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2470-1343&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2470-1343&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2470-1343&client=summon |