Contact order revisited: Influence of protein size on the folding rate

Ivankov, Dmitry N.; Garbuzynskiy, Sergiy O.; Alm, Eric J.; Plaxco, Kevin W.; Baker, David; Finkelstein, Alan

doi:10.1110/ps.0302503

Cited by 345 publications

(430 citation statements)

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“…Much work on the folding rate prediction was published in the pureempirical approach. They include the prediction model based on amino acid sequence [18,2628], based on tertiary structure [15,29] and based on secondary structure [17], etc. The prediction accuracy is generally dependent on the size of database.…”

Section: Results Of Statistical Analysis Of 65 Two-state Protein Foldmentioning

confidence: 99%

“…(10) then the prediction accuracy on folding rate from (1) and (11) will be further increased, the correlation coefficient R between theoretical and experimental logarithm rate for 65 two-state proteins attained 0.78 [57]. [15] and ACO [29] from web server at http://depts.washington.edu/bakerpg/contact_order/. f) Size-modified contact order SMCO=RCO×L 0.7 [29], L, number of residues that have defined three-dimensional coordinates and contribute to the relative contact order (RCO) calculations.…”

Section: Results Of Statistical Analysis Of 65 Two-state Protein Foldmentioning

confidence: 99%

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Statistical analyses of protein folding rates from the view of quantum transition

Luo

2014

Sci. China Life Sci.

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Understanding protein folding rate is the primary key to unlock the fundamental physics underlying protein structure and its folding mechanism. Especially, the temperature dependence of the folding rate remains unsolved in the literature. Starting from the assumption that protein folding is an event of quantum transition between molecular conformations, we calculated the folding rate for all two-state proteins in a database and studied their temperature dependencies. The non-Arrhenius temperature relation for 16 proteins, whose experimental data had previously been available, was successfully interpreted by comparing the Arrhenius plot with the first-principle calculation. A statistical formula for the prediction of two-state protein folding rate was proposed based on quantum folding theory. The statistical comparisons of the folding rates for 65 two-state proteins were carried out, and the theoretical vs. experimental correlation coefficient was 0.73. Moreover, the maximum and the minimum folding rates given by the theory were consistent with the experimental results. quantum folding, protein folding rate, temperature dependence, number of torsion mode, folding free energy Citation:Lv J, Luo LF. Statistical analyses of protein folding rates from the view of quantum transition. Sci China Life Sci, 2014Sci, , 57: 1197Sci, -1212Sci, , doi: 10.1007 It is well known that a protein chain can spontaneously fold into its unique native structure [1,2]. To paraphrase Levinthal's paradox, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a period of time longer than the age of the universe to arrive at its correct native conformation [3]. Apart from theory, it is a fact that experimentally measured times for spontaneous folding of single-domain globular proteins range from microseconds [46] to tens of minutes [7]. Thus, how configurations of proteins are determined and what makes them fold so quickly are questions that constitute a longstanding puzzle in molecular biology. While two prominent models have been proposed to study the protein folding mechanism, folding nucleus [8,9] and folding tunnel [1014], the importance of topology and contact order in protein folding has been recognized over the last 15 years, and many new models to predict the protein folding rate have been published [1529]. Curiously, it is notable that the rate at which proteins fold is highly sensitive to temperature, showing non-Arrhenius behavior, i.e., the temperature dependence of the rate constant is, in fact, not exponential for these reactions. The nonlinearity of logarithm folding rate on temperature 1/T has been conventionally interpreted by the nonlinear temperature dependence of the configurational diffusion constant on rough energy landscapes [30] or by the temperature dependence of hydrophobic interaction [31,32]. Another model was proposed more recently to interpret the difference between folding and unfolding by introducing the number of dena...

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Section: Results Of Statistical Analysis Of 65 Two-state Protein Foldmentioning

confidence: 99%

Section: Results Of Statistical Analysis Of 65 Two-state Protein Foldmentioning

confidence: 99%

Statistical analyses of protein folding rates from the view of quantum transition

Luo

2014

Sci. China Life Sci.

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“…The observation that low "contact order", which implies a high ratio of LIs to NLIs in the folded structures of proteins, is correlated with high rate of folding seems to give strong support to the role of LIs in determining the folding rate (Plaxco et al 1998;Ivankov et al 2003). Weikl (Weikl and Dill 2003;Weikl 2008) introduced the concept of effective contact order and showed that closure of small loops shows improved correlation with the global folding rate.…”

Section: O'neill Et Al (O'neill and Robert Matthews 2000)mentioning

confidence: 98%

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

et al. 2013

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The extremely fast and efficient folding transition (in seconds) of globular proteins led to the search for some unifying principles embedded in the physics of the folding polypeptides. Most of the proposed mechanisms highlight the role of local interactions that stabilize secondary structure elements or a folding nucleus as the starting point of the folding pathways, i.e., a "bottom-up" mechanism. Nonlocal interactions were assumed either to stabilize the nucleus or lead to the later steps of coalescence of the secondary structure elements. An alternative mechanism was proposed, an "up-down" mechanism in which it was assumed that folding starts with the formation of very few non-local interactions which form closed long loops at the initiation of folding. The possible biological advantage of this mechanism, the "loop hypothesis", is that the hydrophobic collapse is associated with ordered compactization which reduces the chance for degradation and misfolding. In the present review the experiments, simulations and theoretical consideration that either directly or indirectly support this mechanism are summarized. It is argued that experiments monitoring the time-dependent development of the formation of specifically targeted early-formed sub-domain structural elements, either long loops or secondary structure elements, are necessary. This can be achieved by the timeresolved FRET-based "double kinetics" method in combination with mutational studies. Yet, attempts to improve the time resolution of the folding initiation should be extended down to the sub-microsecond time regime in order to design experiments that would resolve the classes of proteins which first fold by local or non-local interactions.

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“…One important insight from experimental studies is that for many proteins the rate of folding is inversely correlated to the density of sequence-distant contacts (referred to as "contact order") in the native state [3,15]. This correlation suggests that the overall fold or "topology" of the native-state is established in the rate-limiting step in folding [16].…”

Section: Recent Observations and Related Questions In Folding Of Globmentioning

confidence: 99%

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

Kloss

Courtemanche

Barrick

2008

Archives of Biochemistry and Biophysics

101

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Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings. KeywordsRepeat-protein; Ankyrin repeat; protein folding; energy landscape; atomic force microscopy In the last twenty-five years, advances in experimental studies and in computation and theory have greatly improved our understanding of protein folding. On the experimental side, advances have come from new and improved techniques, including site-directed mutagenesis, hydrogen exchange (HX) methods, improvements to rapid mixing devices, and development of single-molecule fluorescence and force spectroscopy. Experimental advances have also come in the form of generalizations and insights from expanding databases of thermodynamic and kinetic constants for protein folding [1][2][3][4][5].On the computational side, advances in our understanding of protein folding have come from huge increases in computer speed and storage capacity, in innovative methods to study energetics of folding such as ensemble-based approaches and replica exchange methods [6,7], and distributed computing methods [8]. As with experiment, computational studies of folding, and in particular, fold prediction, have greatly benefited from expanding databases of protein structure [9,10]. On the theoretical side, the application of ideas from condensed-matter *Correspondence: barrick@jhu.edu, (410) 516-0409. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptArch Biochem Biophys. Author manuscript; available in PMC 2009 January ...

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Contact order revisited: Influence of protein size on the folding rate

Cited by 345 publications

References 64 publications

Statistical analyses of protein folding rates from the view of quantum transition

Statistical analyses of protein folding rates from the view of quantum transition

The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

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