Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations

Cote, Yoann; Senet, Patrick; Delarue, Patrice; Maisuradze, Gia G.; Scheraga, Harold A.

doi:10.1073/pnas.1013674107

Cited by 30 publications

(40 citation statements)

References 39 publications

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“…For circular geometry, the RCFs are defined (6, 11) as C l;n ðtÞ ¼ hT l ½x n ðt 0 ; t 0 þ tÞi t 0 ≡T l ðx n Þ; [1] where T l ðx n Þ is a Tchebychev polynomial of order l (11). In the present work, the second-order RCFs, T 2 ðxÞ ¼ 2x 2 − 1, were analyzed [results for T 1 ðxÞ ¼ x contain similar information (6)]. In Eq.…”

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“…5 and 6 and in the present work). The mechanism of transport of the particle along the circle, due to random fluctuating torques, is characterized by its MeanSquare-Displacement (MSD) and Rotational Correlation Functions (RCFs) (6). The RCFs associated with γ n are related to the position u n ðtÞ of the fictitious particle on the circle where u n ðtÞ ¼ fcos½γ n ðtÞ; sin½γ n ðtÞg (Fig.…”

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“…mation about the possible dynamical coupling between δ n and γ n . To examine the dynamical correlation, the analogy between the fluctuations over time of a dihedral angle; for example γ n , and Brownian motion on a unit circle (5,6) (Fig. S1B) is exploited.…”

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Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Cote

Senet

Delarue

et al. 2012

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

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Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarsegrained dihedral angles (CGDAs) γ n based on four successive C α atoms (n − 1, n, n þ 1, n þ 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δ n formed by the virtual bond joining two consecutive C α atoms (n, n þ 1) and the bonds joining these C α atoms to their respective C β atoms] was analyzed. The motions of SCs (δ n ) and MC (γ n ) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δ n ) and those of the MC (γ n ) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the δ n ðtÞ and γ n ðtÞ time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [δðtÞ and γðtÞ time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding.dihedral principal component analysis | free-energy landscape | power law | subdiffusion T he motions of the side chains and of the backbone of a protein are coupled to each other in protein folding. The removal of the nonpolar side chains from the solvent in protein folding orients the backbone locally (1), and the formation of the backbone hydrogen bonds between residues in the secondary structures induces displacements of their side chains. Therefore, in order to understand protein folding, it is necessary to understand how the motions of the side chains are propagated to the backbone and vice versa. As a prerequisite, it is necessary to understand how the motions of the side chains are coupled to those of the main chain in the native state of a protein. To address this question, five 80 ns all-atom molecular dynamics (MD) simulations of a 46-residue α/β model protein VA3 (PDB: 1ED0) (2) in its native state were analyzed. Protein VA3 was chosen here because it is highly homologous to the well-studied protein crambin, but unlike crambin (3), it is soluble in water (2).To express the correlation between the main-chain and the side-chain motions quantitatively, two coarse-grained dihedral angles (CGDAs) were defined for each residue n (Fig. S1A). The angles characterizing the fluctuations of the main chain are the CGDAs γ n (4-6) formed by the virtual bonds joining four consecutive C α atoms (n − 1, n, n þ 1 and n þ 2) along the amino acid sequence with 2 ≤ n ≤ N − 2 and N being the number of residues (Fig. S1A). The angles γ n are coordinates used to describe large changes o...

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Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Cote

Senet

Delarue

et al. 2012

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

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“…Structural fluctuations are essential for the function of proteins in the native state, as well as for correct folding. As we demonstrated in earlier work (38), analysis of structural fluctuations near the native state of a protein can also provide insight into its dynamical behavior. To examine the fluctuations, thermostability, and unfolding processes of these proteins, all-atom MD simulations starting from the experimental structures were carried out using the CHARMM36 force field.…”

Section: Resultsmentioning

confidence: 97%

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Maisuradze

Yin

et al. 2017

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

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We recently introduced a physically based approach to sequence comparison, the property factor method (PFM). In the present work, we apply the PFM approach to the study of a challenging set of sequences-the bacterial chemotaxis protein CheY, the N-terminal receiver domain of the nitrogen regulation protein NT-NtrC, and the sporulation response regulator Spo0F. These are all response regulators involved in signal transduction. Despite functional similarity and structural homology, they exhibit low sequence identity. PFM sequence comparison demonstrates a statistically significant qualitative difference between the sequence of CheY and those of the other two proteins that is not found using conventional alignment methods. This difference is shown to be consonant with structural characteristics, using distance matrix comparisons. We also demonstrate that residues participating strongly in native contacts during unfolding are distributed differently in CheY than in the other two proteins. The PFM result is also in accord with dynamic simulation results of several types. Molecular dynamics simulations of all three proteins were carried out at several temperatures, and it is shown that the dynamics of CheY are predicted to differ from those of NT-NtrC and Spo0F. The predicted dynamic properties of the three proteins are in good agreement with experimentally determined B factors and with fluctuations predicted by the Gaussian network model. We pinpoint the differences between the PFM and traditional sequence comparisons and discuss the informatic basis for the ability of the PFM approach to detect physical differences between these sequences that are not apparent from traditional alignment-based comparison.amino acid physical properties | protein fluctuations | all-atom simulations

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“…This work is being carried out by Gia Maisuradze, a research associate, and Adam Liwo. Dynamics of fluctuations in the native state of a protein are being examined by Patrick Senet (117), a visiting scientist, and by Cote et al (143). Much of our recent work on dynamics has been summarized in two review chapters (48,112).…”

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Respice, Adspice, and Prospice

Scheraga

2011

Annu. Rev. Biophys.

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The title, "Look to the past, Look to the present, and Look to the future," the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.

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Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations

Cited by 30 publications

References 39 publications

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Respice, Adspice, and Prospice

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