title: Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts.
abstract: 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(8) and Lys(12), the individually weak, nonspecific interactions with lysines together stabilize the charged Asp(8), leading to a pKa 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.
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.
authors.forename: Chuanyin
authors.initials: C
authors.lastname: Shi
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland. Electronic address: jshen@rx.umaryland.edu.
authors.forename: Jana
authors.initials: J
authors.lastname: Shen
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D058767:Protein Unfolding; D012269:Ribosomal Proteins / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D010455:Peptides; D012269:Ribosomal Proteins; C049650:ribosomal protein L9