Single-mutation-induced stability loss in protein lysozyme

2007 ◽  
Vol 35 (6) ◽  
pp. 1551-1557 ◽  
Author(s):  
L. Ye ◽  
Z. Wu ◽  
M. Eleftheriou ◽  
R. Zhou

Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.

1938 ◽  
Vol 34 (2) ◽  
pp. 238-252 ◽  
Author(s):  
J. S. Wang

The statistical theory of long-range interactions between adsorbed particles on a plane lattice is worked out approximately, by treating in detail the distribution of adsorbed particles among a few sites inside and on the boundary of a circular region, and regarding the distribution outside the circle as uniform and continuous with a density Kθ per unit area, where K is the number of lattice points per unit area and θ is the fraction of surface covered by adsorbed particles. The continuous distribution begins at a distance ρ from the centre of the circle, ρ being determined by the condition that the probability of occupation of a first shell site is equal to the probability θ of occupation of the central site. Using this method, general formulae for the adsorption isotherm and the heat of adsorption are obtained. Numerical applications for dipole interactions and for quadratic and hexagonal lattices are worked out in detail and the case in which the dipole moment varies with θ is discussed.


2013 ◽  
Vol 27 (24) ◽  
pp. 1350143 ◽  
Author(s):  
MIRABEAU SAHA ◽  
TIMOLEON C. KOFANÉ

In this paper, the comparison between power-law long-range interaction and Kac–Baker long-range interaction in the DNA molecule is investigated. This is done by employing an extended version of spin-like model of the DNA molecule with long-range interaction between intra-strand nucleotides and helicoidal coupling between inter-strand nucleotides when an RNA-polymerase binds to the DNA at biological temperature. Results show that LRIs have an undeniable effect on the DNA dynamics and that one is free to use either PLLRI or KBLRI to study DNA behaviors.


2007 ◽  
Vol 104 (14) ◽  
pp. 5824-5829 ◽  
Author(s):  
R. Zhou ◽  
M. Eleftheriou ◽  
A. K. Royyuru ◽  
B. J. Berne

Author(s):  
Ting XIE ◽  
Andrea Orbán ◽  
Xiaodong Xing ◽  
Eliane Luc-Koenig ◽  
Romain Vexiau ◽  
...  

Abstract Ultracold temperatures in dilute quantum gases opened the way to an exquisite control of matter at the quantum level. Here we focus on the control of ultracold atomic collisions using a laser to engineer their interactions at large interatomic distances. We show that the entrance channel of two colliding ultracold atoms can be coupled to a repulsive collisional channel by the laser light so that the overall interaction between the two atoms becomes repulsive: this prevents them to come close together and to undergo inelastic processes, thus protecting the atomic gases from unwanted losses. We illustrate such an optical shielding mechanism with 39K and 133Cs atoms colliding at ultracold temperature (<1 microkelvin). The process is described in the framework of the dressed-state picture and we then solve the resulting stationary coupled Schrödinger equations. The role of spontaneous emission and photoinduced inelastic scattering is also investigated as possible limitations of the shielding efficiency. We predict an almost complete suppression of inelastic collisions over a broad range of Rabi frequencies and detunings from the 39K D2 line of the optical shielding laser, both within the [0, 200 MHz] interval. We found that the polarization of the shielding laser has a minor influence on this efficiency. This proposal could easily be formulated for other bialkali-metal pairs as their long-range interaction are all very similar to each other.


2005 ◽  
Vol 12 (2) ◽  
pp. 171-180 ◽  
Author(s):  
M. P. Leubner ◽  
Z. Vörös

Abstract. The observed scale dependence of the probability distributions of the differences of characteristic solar wind variables is analyzed. Intermittency of the turbulent fluctuations at small-scale spatial separations is accompanied by strongly non-Gaussian distributions that turn into a normal distribution for large-scale separation. Conventional theoretical models are subject to insufficient physical justification since nonlocality in turbulence should be based on long-range interactions, provided recently by the bi-kappa distribution in the context of nonextensive thermo-statistics. Observed WIND and ACE probability distributions are accurately reproduced for different time lags by the one-parameter bi-kappa functional, a core-halo convolution, where kappa measures the degree of nonlocality or nonextensivity in the system. Gradual decoupling is obtained by enhancing the spatial separation scale corresponding to increasing kappa values, where a Gaussian is approached for infinite kappa. Consequently, long-range interactions introduced on the fundamental level of entropy generalization, are able to provide physically the source of the observed scale dependence of the turbulent fluctuations in the intermittent interplanetary medium.


2008 ◽  
Vol 82 (18) ◽  
pp. 9008-9022 ◽  
Author(s):  
Sinéad Diviney ◽  
Andrew Tuplin ◽  
Madeleine Struthers ◽  
Victoria Armstrong ◽  
Richard M. Elliott ◽  
...  

ABSTRACT The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5′ and 3′ noncoding regions (5′ and 3′ NCRs) and in the NS5B coding sequence. Through the application of several algorithmically independent bioinformatic methods to detect phylogenetically conserved, thermodynamically favored RNA secondary structures, we demonstrate a long-range interaction between sequences in the previously described CRE (5BSL3.2, now SL9266) with a previously predicted unpaired sequence located 3′ to SL9033, approximately 200 nucleotides upstream. Extensive reverse genetic analysis both supports this prediction and demonstrates a functional requirement in genome replication. By mutagenesis of the Con-1 replicon, we show that disruption of this alternative pairing inhibited replication, a phenotype that could be restored to wild-type levels through the introduction of compensating mutations in the upstream region. Substitution of the CRE with the analogous region of different genotypes of HCV produced replicons with phenotypes consistent with the hypothesis that both local and long-range interactions are critical for a fundamental aspect of genome replication. This report further extends the known interactions of the SL9266 CRE, which has also been shown to form a “kissing loop” interaction with the 3′ NCR (P. Friebe, J. Boudet, J. P. Simorre, and R. Bartenschlager, J. Virol. 79:380-392, 2005), and suggests that cooperative long-range binding with both 5′ and 3′ sequences stabilizes the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.


Open Physics ◽  
2009 ◽  
Vol 7 (3) ◽  
Author(s):  
William Thistleton ◽  
John Marsh ◽  
Kenric Nelson ◽  
Constantino Tsallis

AbstractWe study a strictly scale-invariant probabilistic N-body model with symmetric, uniform, identically distributed random variables. Correlations are induced through a transformation of a multivariate Gaussian distribution with covariance matrix decaying out from the unit diagonal, as ρ/r α for r =1, 2, ..., N-1, where r indicates displacement from the diagonal and where 0 ⩽ ρ ⩽ 1 and α ⩾ 0. We show numerically that the sum of the N dependent random variables is well modeled by a compact support q-Gaussian distribution. In the particular case of α = 0 we obtain q = (1-5/3 ρ) / (1- ρ), a result validated analytically in a recent paper by Hilhorst and Schehr. Our present results with these q-Gaussian approximants precisely mimic the behavior expected in the frame of non-extensive statistical mechanics. The fact that the N → ∞ limiting distributions are not exactly, but only approximately, q-Gaussians suggests that the present system is not exactly, but only approximately, q-independent in the sense of the q-generalized central limit theorem of Umarov, Steinberg and Tsallis. Short range interaction (α > 1) and long range interactions (α < 1) are discussed. Fitted parameters are obtained via a Method of Moments approach. Simple mechanisms which lead to the production of q-Gaussians, such as mixing, are discussed.


1995 ◽  
Vol 283 ◽  
pp. 43-95 ◽  
Author(s):  
P. K. Yeung ◽  
James G. Brasseur ◽  
Qunzhen Wang

As discussed in a recent paper by Brasseur & Wei (1994), scale interactions in fully developed turbulence are of two basic types in the Fourier-spectral view. The cascade of energy from large to small scales is embedded within ‘local-to-non-local’ triadic interactions separated in scale by a decade or less. ‘Distant’ triadic interactions between widely disparate scales transfer negligible energy between the largest and smallest scales, but directly modify the structure of the smallest scales in relationship to the structure of the energy-dominated large scales. Whereas cascading interactions tend to isotropize the small scales as energy moves through spectral shells from low to high wavenumbers, distant interactions redistribute energy within spectral shells in a manner that leads to anisotropic redistributions of small-scale energy and phase in response to anisotropic structure in the large scales. To study the role of long-range interactions in small-scale dynamics, Yeung & Brasseur (1991) carried out a numerical experiment in which the marginally distant triads were purposely stimulated through a coherent narrow-band anisotropic forcing at the large scales readily interpretable in both the Fourier- and physical-space views. It was found that, after one eddy turnover time, the smallest scales rapidly became anisotropic as a direct consequence of the marginally distant triadic group in a manner consistent with the distant triadic equations. Because these asymptotic equations apply in the infinite Reynolds number limit, Yeung & Brasseur argued that the observed long-range effects should be applicable also at high Reynolds numbers.We continue the analysis of forced simulations in this study, focusing (i) on the detailed three-dimensional restructuring of the small scales as predicted by the asymptotic triadic equations, and (ii) on the relationship between Fourier- and physical-space evolution during forcing. We show that the three-dimensional restructuring of small-scale energy and vorticity in Fourier space from large-scale forcing is predicted in some detail by the distant triadic equations. We find that during forcing the distant interactions alter small-scale structure in two ways: energy is redistributed anisotropically within high-wavenumber spectral shells, and phase correlations are established at the small scales by the distant interactions. In the numerical experiments, the long-range interactions create two pairs of localized volumes of concentrated energy in three-dimensional Fourier space at high wavenumbers in which the Fourier modes are phase coupled. Each pair of locally phase-correlated volumes of Fourier modes separately corresponds to aligned vortex tubes in physical space in two orthogonal directions. We show that the dynamics of distant interactions in creating small-scale anisotropy may be described in physical space by differential advection and distortion of small-scale vorticity by the coherent large-scale energy-containing eddies, producing anisotropic alignment of small-scale vortex tubes.Scaling arguments indicate a disparity in timescale between distant triadic interactions and energy-cascading local-to-non-local interactions which increases with scale separation. Consequently, the small scales respond to forcing initially through the distant interactions. However, as energy cascades from the large-scale to the small-scale Fourier modes, the stimulated distant interactions become embedded within a sea of local-to-non-local energy cascading interactions which reduce (but do not eliminate) small-scale anisotropy at later times. We find that whereas the small-scale structure is still anisotropic at these later times, the second-order velocity moment tensor is insensitive to this anisotropy. Third-order moments, on the other hand, do detect the anisotropy. We conclude that whereas a single statistical measure of anisotropy can be used to indicate the presence of anisotropy, a null result in that measure does not necessarily imply that the signal is isotropic. The results indicate that non-equilibrium non-stationary turbulence is particularly sensitive to long-range interactions and deviations from local isotropy.


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