Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
Identifieur interne : 000A93 ( PubMed/Curation ); précédent : 000A92; suivant : 000A94Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
Auteurs : Leonardo Vazquez [Brésil] ; Luis Mauricio Trambaioli Da Rocha E Lima [Brésil] ; Marcius Da Silva Almeida [Brésil]Source :
- PloS one [ 1932-6203 ] ; 2017.
Descripteurs français
- KwdFr :
- Biosynthèse des protéines, Dichroïsme circulaire, Diffraction des rayons X, Diffusion aux petits angles, Interactions hydrophobes et hydrophiles, Modèles moléculaires, Peptides (), Pliage des protéines, Protéines de fusion recombinantes (), Protéines virales non structurales (), Spectroscopie par résonance magnétique, Structure secondaire des protéines, Structure tertiaire des protéines, Séquence d'acides aminés, Virus du SRAS ().
- MESH :
- Biosynthèse des protéines, Dichroïsme circulaire, Diffraction des rayons X, Diffusion aux petits angles, Interactions hydrophobes et hydrophiles, Modèles moléculaires, Peptides, Pliage des protéines, Protéines de fusion recombinantes, Protéines virales non structurales, Spectroscopie par résonance magnétique, Structure secondaire des protéines, Structure tertiaire des protéines, Séquence d'acides aminés, Virus du SRAS.
English descriptors
- KwdEn :
- Amino Acid Sequence, Circular Dichroism, Hydrophobic and Hydrophilic Interactions, Magnetic Resonance Spectroscopy, Models, Molecular, Peptides (chemistry), Protein Biosynthesis, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Fusion Proteins (chemistry), SARS Virus (chemistry), Scattering, Small Angle, Viral Nonstructural Proteins (chemistry), X-Ray Diffraction.
- MESH :
- chemical , chemistry : Peptides, Recombinant Fusion Proteins, Viral Nonstructural Proteins.
- chemistry : SARS Virus.
- Amino Acid Sequence, Circular Dichroism, Hydrophobic and Hydrophilic Interactions, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Biosynthesis, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Scattering, Small Angle, X-Ray Diffraction.
Abstract
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
DOI: 10.1371/journal.pone.0182132
PubMed: 28750053
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domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28750053</PMID><DateCompleted><Year>2017</Year><Month>10</Month><Day>04</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>7</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.</ArticleTitle><Pagination><MedlinePgn>e0182132</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0182132</ELocationID><Abstract><AbstractText>The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vazquez</LastName><ForeName>Leonardo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>E Lima</LastName><ForeName>Luis Mauricio Trambaioli da Rocha</ForeName><Initials>LMTDR</Initials><AffiliationInfo><Affiliation>Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Almeida</LastName><ForeName>Marcius da Silva</ForeName><Initials>MDS</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-4921-8185</Identifier><AffiliationInfo><Affiliation>Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>07</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053838" MajorTopicYN="N">Scattering, Small Angle</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017361" MajorTopicYN="N">Viral Nonstructural Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014961" MajorTopicYN="N">X-Ray Diffraction</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>04</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>07</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>7</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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