β-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease

A shorter peptide model from staphylococcal nuclease for the folding–unfolding equilibrium of a β-hairpin shows that unfolded state has significant contribution from compact conformational states

“…In both the cases, the initial folding event involves the formation of YP contact resulting in loop conformation for YKGQP (Patel et al, 2006). The same YP contact is also observed in the simulation of shorter pentapeptide YKGQP (Patel and Sasidhar, 2007).…”

“…events (Patel et al, 2006). However, in the current simulation the interconversion between native and non-native hairpin is also observed.…”

“…Consolidation of hydrophobic interactions and subsequent formation of hydrogen bonds are also common to both LMYKGQPM and DTVKLMYKGQPMTFR peptides suggesting that in both the cases local interactions involved in the loop formation are guiding the process of folding. In the simulation of the bigger peptide DTVKLMYKGQPMTFR, no unfolding events are observed during the reported time of the simulation (Patel et al, 2006) perhaps due to vary low unfolding rate caused by strong hydrophobic interaction as suggested in the literature (Du et al, 2004). However, in the current truncated peptide elimination of a few hydrophobic interactions as explained in Section 1 should have resulted in increased unfolding rate and thus we have been able to observe many folding and unfolding events.…”

“…We have recently studied the hairpin peptide DTVKLM YKGQPMTFR from staphylococcal nuclease and this peptide folds into hairpin-like conformation with native-like and non-native hairpin conformations (Patel et al, 2006). In these simulations, once the peptide folds into hairpin conformation starting from extended or polyproline II conformation the hairpin does not unfold during the reported simulation times.…”

Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study

“…For instance, peptide fragments involved in nucleation of their parent protein folding have been shown to adopt their inherent native fold even in the absence of the protein context. A series of molecular dynamics s t u d i e s o n t h e f o l d i n g a β -h a i r p i n s e q u e n c e ( 21 DTVKLMYKGQPMTFR 35 ) [2], from staphylococcal nuclease, and different fragments corresponding to its turn region (YKGQP [3] and YKGQ [4]) showed that their intrinsic hairpin and turn propensities, respectively, were maintained even without the complete protein context indicating the importance of the primary sequence in determining the conformation adopted by the peptide fragment. It is also known that apart from the primary sequence, environmental factors like tertiary contacts within the folded protein, solvent polarity, ions, pH, temperature etc.…”