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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Schweitzer-stenner, Reinhard Meral, Derya Verbaro, Daniel Urbanc, Brigita Toal, Siobhan |
| Description | Author Affiliation: Toal S ( Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA.) |
| Abstract | Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H( ))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations. |
| ISSN | 15206106 |
| e-ISSN | 15205207 |
| Journal | The Journal of Physical Chemistry B |
| Issue Number | 14 |
| Volume Number | 117 |
| Language | English |
| Publisher | American Chemical Society (United States) |
| Publisher Date | 2013-04-11 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Dipeptides Chemistry Oligopeptides Protons Circular Dichroism Hydrogen-Ion Concentration Magnetic Resonance Spectroscopy Molecular Dynamics Simulation Peptides Protein Conformation Protein Folding Thermodynamics Vibration Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Physical chemistry |
| Content Type | Text |
| Resource Type | Article |
| Subject | Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry |
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