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Nascent [Beta]-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts

Despite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations... Full description

Journal Title: Biophysical Journal Aug 4, 2015, Vol.109(3), p.630
Main Author: Chen, Wei
Other Authors: Shi, Chuanyin , Shen, Jana
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 00063495 ; E-ISSN: 15420086
Link: http://search.proquest.com/docview/1702861331/?pq-origsite=primo
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title: Nascent [Beta]-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts
format: Article
creator:
  • Chen, Wei
  • Shi, Chuanyin
  • Shen, Jana
subjects:
  • Peptides
  • Proteins
  • Hydrogen Bonds
  • Electrostatics
ispartof: Biophysical Journal, Aug 4, 2015, Vol.109(3), p.630
description: Despite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1-22) and NTL9(6-17). We found that while NTL9(6-17) is unstructured, NTL9(1-22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp... and Lys..., the individually weak, nonspecific interactions with lysines together stabilize the charged Asp..., leading to a pK... shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1-22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters. (ProQuest: ... denotes formulae/symbols omitted.)
language: eng
source:
identifier: ISSN: 00063495 ; E-ISSN: 15420086
fulltext: fulltext
issn:
  • 00063495
  • 0006-3495
  • 15420086
  • 1542-0086
url: Link


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titleNascent [Beta]-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts
creatorChen, Wei ; Shi, Chuanyin ; Shen, Jana
ispartofBiophysical Journal, Aug 4, 2015, Vol.109(3), p.630
identifierISSN: 00063495 ; E-ISSN: 15420086
subjectPeptides ; Proteins ; Hydrogen Bonds ; Electrostatics
descriptionDespite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1-22) and NTL9(6-17). We found that while NTL9(6-17) is unstructured, NTL9(1-22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp... and Lys..., the individually weak, nonspecific interactions with lysines together stabilize the charged Asp..., leading to a pK... shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1-22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters. (ProQuest: ... denotes formulae/symbols omitted.)
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descriptionDespite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1-22) and NTL9(6-17). We found that while NTL9(6-17) is unstructured, NTL9(1-22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp... and Lys..., the individually weak, nonspecific interactions with lysines together stabilize the charged Asp..., leading to a pK... shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1-22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters. (ProQuest: ... denotes formulae/symbols omitted.)
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titleNascent [Beta]-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts
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abstractDespite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1-22) and NTL9(6-17). We found that while NTL9(6-17) is unstructured, NTL9(1-22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp... and Lys..., the individually weak, nonspecific interactions with lysines together stabilize the charged Asp..., leading to a pK... shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1-22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters. (ProQuest: ... denotes formulae/symbols omitted.)
copNew York
pubBiophysical Society
urlhttp://search.proquest.com/docview/1702861331/
doi10.1016/j.bpj.2015.06.035
pages630-638
date2015-08-04