Dynamics of the helix-coil transition in poly-L-ornithine

Hammes, Gordon G.; Roberts, Peter

doi:10.1021/ja01035a036

Cited by 95 publications

(45 citation statements)

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“…This value is comparable to the folding rate of phage 434 Cro protein (12). Structural transitions in partly folded peptides are much faster; for example, the slow nucleation step in helix formation by poly L-ornithine is 10 5 times faster (13).…”

Section: Discussionmentioning

confidence: 79%

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Osa

Bateman

et al. 2007

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

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Can unique protein structures arise from a limited set of amino acids present on the prebiotic Earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited ''alphabet'' of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic Earth.four-helix bundle ͉ NMR spectroscopy ͉ protein stability ͉ chemical evolution ͉ protein folding I n the prebiotic Earth, hydrophobic and charged amino acids were thought to have been rather common, whereas polar amino acids were rare (1, 2). Could such a limited set of amino acids have given rise to unique well folded proteins? To gain insight into this question, we have studied the conformational stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala, plus a -Gly-Gly-Tyr extension for concentration determination, which self-associates to form a well packed, four-helix bundle protein.KIA7 was previously identified from a combinatorial peptide library as having a highly helical structure (as gauged by CD), a well packed hydrophobic core (1-anilino-8-naphthalene sulfonate fluorescence), and a specific tetrameric quaternary structure (analytical ultracentrifugation) (3, 4). The positively charged lysine side chains prevent the formation of higherordered oligomers. Because no tertiary hydrogen bonds, higherorder oligomerization or crystal packing interactions, or favorable electrostatic interactions are present in KIA7, this study constitutes a test of whether or not a specific, unique structure can arise from a highly limited set of stabilizing interactions, namely, the hydrophobic effect and van der Waals interactions.In addition to KIA7, two other members of the KIA series of peptides, KIA5 and KIA10, were studied (Table 1). These peptides are variants of the KIA7 sequence and possess lesser degrees of ordered structure (3). A stabilized KIA7 variant with a disulfide cross-link, CG 3 KIA7, was also examined, and additional peptides truncating the -Gly-Gly-Tyr C-terminal extension, KIA7⌬, or carrying Tyr to Phe, KIA7F, or Tyr to Ile, KIA7I, substitutions were studied to probe the possible stabilizing or struc...

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Section: Discussionmentioning

confidence: 79%

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Osa

Bateman

et al. 2007

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

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“…7 X I 0 -8 sec, while the rate constant for the format ion of a helical segment at the end of a helical section was evaluated to be 7.4 X 10-10 sec. 30 2.6. Hydrated Protein Powders Some interesting events have been detected by NMR and dielectric measurements in protein powders during the hydration process.…”

Section: S Helix-coil Transition Rates In Polypeptidesmentioning

confidence: 99%

Statistical Time Events in Enzymes: A Physical Assessmen

Careri

Fasella

Gratton

et al. 1975

CRC Critical Reviews in Biochemistry

200

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“…This rapid folding phase has been detected by circular dichroism (CD), fluorescence, and NMR stopped-flow studies in many proteins and reflects the potential for proteins to fold on the submillisecond time scale (3)(4)(5)(6)(7)(8)(9). Ultrasonic attenuation and dielectric relaxation measurements indicate that isolated a-helices fold with relaxation times of 10-7 to 10-8 s, four to five orders of magnitude faster than rate constants observable by stopped-flow methods (10)(11)(12). This vast time-scale difference represents a major gap in our understanding of the fundamental early events in folding.…”

mentioning

confidence: 99%

Submillisecond folding of monomeric lambda repressor.

Huang

Oas

1995

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

247

169

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The folding kinetics of a truncated form of the N-terminal domain of phage A repressor [A6-s] has been investigated by using the technique of dynamic NMR. A6-85 has been shown previously to fold in a purely two-state fashion. This allows the determination of folding and unfolding rates from simulation ofthe exchange-broadened aromatic resonances of Tyr-22. The folding kinetics were determined over a range of 1.35 to 3.14 M urea. The urea dependence of both folding and unfolding rate constants is exponential, suggesting that the rate-determining step is invariant at the urea concentrations studied. The folding and unfolding rates extrapolated to 0 M urea at 37°C are 3600 ± 400 s-1 and 27 ± 6 s-1, respectively. The elucidation of the mechanism by which proteins fold remains one of the most challenging problems of modern biology. The earliest events in protein folding are particularly difficult to study by current methods and can be important determininants of the overall reaction (1, 2). Time-resolved kinetic studies have established that many of these important early events occur in <1 ms and are complete within the dead time of the stopped-flow technique. This rapid folding phase has been detected by circular dichroism (CD), fluorescence, and NMR stopped-flow studies in many proteins and reflects the potential for proteins to fold on the submillisecond time scale (3-9). Ultrasonic attenuation and dielectric relaxation measurements indicate that isolated a-helices fold with relaxation times of 10-7 to 10-8 s, four to five orders of magnitude faster than rate constants observable by stopped-flow methods (10)(11)(12). This vast time-scale difference represents a major gap in our understanding of the fundamental early events in folding.In principle, dynamic NMR methods can fill this time-scale gap. Exchange processes that interconvert chemically or conformationally distinct species on the 10-ms to 10-ps time scale can have profound effects on the shape and position of NMR peaks (13). Much faster processes, including motions of the fully native form, can be studied by relaxation time measurements (14-17). To date, dynamic NMR has not been used to measure overall protein folding rates, although it has been used to detect a folding intermediate of rat intestinal fatty acid-binding protein (18). Dynamic NMR-based protein folding studies are rare because the overall folding rates of mostThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.proteins are not fast enough to broaden NMR resonances (19)(20)(21)(22).However, there is a growing number of proteins observed to fold on the microsecond time scale (3, 23-25), and it is likely that their folding processes are similar to early folding events in proteins that fold more slowly. An example of a fast-folding protein is the N-terminal domain (residues 1-102) of bacteriophage A repressor cI, which has been use...

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Dynamics of the helix-coil transition in poly-L-ornithine

Cited by 95 publications

References 2 publications

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Statistical Time Events in Enzymes: A Physical Assessmen

Submillisecond folding of monomeric lambda repressor.

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