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Backbone and side‐chain dynamics of residues in a partially folded β‐sheet peptide from platelet factor‐4
Author(s) -
Daragan Vladimir A.,
Ilyina Elena E.,
Fields Cynthia G.,
Fields Gregg B.,
Mayo Kevin H.
Publication year - 1997
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560060211
Subject(s) - chemistry , side chain , peptide , relaxation (psychology) , folding (dsp implementation) , crystallography , proton nmr , stereochemistry , organic chemistry , polymer , biochemistry , psychology , social psychology , electrical engineering , engineering
Structurally characterizing partially folded states is problematic given the nature of these transient species. A peptide 20mer, T 38 AQLIATLKNGRKISLDLQA 57 (P20), which has been shown to partially fold in a relatively stable turn/loop conformation (LKNGR) and transient β‐sheet structure, is a good model for studying backbone and side‐chain mobilities in a transiently folded peptide by using l3 C‐NMR relaxation. Here, four residues in P20, A43, T44, G48, and 151, chosen for their positions in or near the loop conformation and for compositional variety, have been selectively 13 C‐enriched. Proton‐coupled and decoupled 13 C‐NMR relaxation experiments have been performed to obtain the temperature dependencies (278 K to 343 K) of auto‐ and cross‐correlation motional order parameters and correlation times. In order to differentiate sequence‐neighbor effects from folding effects, two shorter peptides derived from P20, IATLK (P5) and NGRKIS (P6), were similarly l3 C‐enriched and investigated. For A43, T44, G48, and 151 residues in P20 relative to those in P5/P6, several observations are consistent with partial folding in P20: (1) C α H motional tendencies are all about the same, vary less with temperature, and are relatively more restricted, (2) G48 C α H 2 ϕ(t),Ψ(t) rotations are more correlated, and (3) methyl group rotations are slower and yield lower activation energies consistent with formation of hydrophobic “pockets.” In addition, T44 and 151 C β H mobilities in P20 are more restricted at lower temperature than those of their C α H and display significantly greater sensitivity to temperature suggesting a larger enthalpic contribution to side‐chain mobility. Moreover, at higher temperatures, side‐chain methyls and methylenes in P20 are more motionally restricted than those in P5/P6, suggesting that some type of “folded” or “collapsed” structure remains in P20 for what normally would be considered an “unfolded” state.