Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance

Bradley, Erin K.; Thomason, John; Cohen, Fred E.; Kosen, Phyllis Anne; Kuntz, Irwin D.

doi:10.1016/s0022-2836(05)80172-x

Cited by 172 publications

(155 citation statements)

References 62 publications

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“…These values are slightly lower than the rate constants observed for formation of i, i ϩ 6 interactions in polyserine model chains at 5°C (39), which is expected, taking into account that loop formation in the helical peptides involves interior parts of the chain, which are less flexible than the ends (30). The results from the TTET experiments reveal higher helix content in the central part of the helix compared with the termini, which is in agreement with helix-coil theory (11,10) and has previously been observed experimentally by amide hydrogen exchange (32,40), by NMR spectroscopy (41,42), and by electron spin resonance (43). The k f and k u values determined for the different peptides allow the determination of local helix stability.…”

Section: Resultssupporting

confidence: 87%

Local conformational dynamics in α-helices measured by fast triplet transfer

Fierz

Reiner

Kiefhaber

2009

Proc. Natl. Acad. Sci. U.S.A.

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Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in ␣-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 s at 5°C. Local helix formation occurs with a time constant of Ϸ400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with positionindependent elementary time constants of Ϸ50 ns for the addition and of Ϸ65 ns for the removal of an ␣-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.␣-helix-coil transition ͉ protein dynamics ͉ protein folding ͉ triplet-triplet energy transfer

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Section: Resultssupporting

confidence: 87%

Local conformational dynamics in α-helices measured by fast triplet transfer

Fierz

Reiner

Kiefhaber

2009

Proc. Natl. Acad. Sci. U.S.A.

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“…Conditions used were 22"C, pH 2.5, H,O/D,O (9: 1 by vol. (Bradley et al, 1990;Saulitis and Liepins, 1990). The temperature coefficients are all within the range measured for model peptides (Jimtnez et al, 1986).…”

Section: Thermolysin 245-260supporting

confidence: 56%

CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Jiménez

Bruix

González

et al. 1993

European Journal of Biochemistry

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The propensity of the peptide fragments 233-248, 245-260, 258-276, 279-298 and 299-316 from the thermolysin C-terminal domain to form non-random structures has been examined by CD and two-dimensional NMR spectroscopy. The conformational properties of these fragments have been studied in aqueous solution and in the mixed solvent trifluoroethanol/H,O (3 : 7 by vol.). Small but detectable populations of helical structures (up to 10-20%) in aqueous solution have been found for the fragments 233-248,279-298 and 299-316. These populations are remarkably enhanced (50-70%) in the more hydrophobic mixed solvent, where the fragment 258-276 also forms a comparable helical population. These four fragments are helical in the native crystal structure and the spanning of the corresponding helices in the isolated peptides in solution matches very closely the ones in the native structure. In contrast, the fragment 245-260, an D-loop in the crystal, remains unstructured in both solvents. Medium-range NOE between protons in sidechains indicate the adoption of preferred sidechain conformations accompanying helix formation. Results are in agreement with the framework model of folding, in which native elements of secondary structure are formed first and folding follows from the collapse of these structural elements.

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“…Inspection of the relative intensities of the sequential d ␣N NOEs compared with d NN and the medium-range d ␣N (i, iϩ3) NOEs compared with d ␣␤ (i, iϩ3) are stronger than one would expect for an ideal stable helix and imply the occurrence of a dynamic equilibrium between helical and non-helical structures. The helical population for the helical region found above between residues 17 to 32 can be estimated from the ratios of the integrated intensities of the sequential d ␣N and d NN following a procedure enumerated previously (73). This affords ϳ89% (Ϯ 9%) on average over the pairs of residues 17/18, 20/21, 26/27, 31/32, and 32/33 observed for the helix in Vpr .…”

Section: Discussionmentioning

confidence: 96%

Structural Characterization of the HIV-1 Vpr N Terminus

Bruns

Fossen

Wray

et al. 2003

Journal of Biological Chemistry

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The 96-residue human immunodeficiency virus (HIV) accessory protein Vpr serves manifold functions in the retroviral life cycle including augmentation of viral replication in non-dividing host cells, induction of G 2 cell cycle arrest, and modulation of HIV-induced apoptosis. Using a combination of dynamic light scattering, circular dichroism, and NMR spectroscopy the N terminus of Vpr is shown to be a unique domain of the molecule that behaves differently from the C-terminal domain in terms of self-association and secondary structure folding. Interestingly, the four highly conserved proline residues in the N terminus are predicted to have a high propensity for cis/trans isomerism. Thus the high resolution structure and folding of a synthetic N-terminal peptide (Vpr 1-40 ) and smaller fragments thereof have been investigated. 1 H NMR data indicate Vpr 1-40 possesses helical structure between residues 17-32, and for the first time, this helix, which is bound by proline residues, was observed even in aqueous solution devoid of any detergent supplements. In addition, NMR data revealed that all of the proline residues undergo a cis/ trans isomerism to such an extent that ϳ40% of all Vpr molecules possess at least one proline in a cis conformation. This phenomenon of cis/trans isomerism, which is unprecedented for HIV-1 Vpr, not only provides an explanation for the molecular heterogeneity observed in the full-length molecule but also indicates that in vivo the folding and function of Vpr should depend on a cis/trans-proline isomerase activity, particularly as two of the proline residues in positions 14 and 35 show considerable amounts of cis isomers. This prediction correlates well with our recent observation

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Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance

Cited by 172 publications

References 62 publications

Local conformational dynamics in α-helices measured by fast triplet transfer

Local conformational dynamics in α-helices measured by fast triplet transfer

CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Structural Characterization of the HIV-1 Vpr N Terminus

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Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance

Cited by 172 publications

References 62 publications

Local conformational dynamics in α-helices measured by fast triplet transfer

Local conformational dynamics in α-helices measured by fast triplet transfer

CD and 1H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin

Structural Characterization of the HIV-1 Vpr N Terminus

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CD and ¹H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin