Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A

AbstractProteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason—besides the well-known problem with the description of single file pore water—why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model

A divide-and-conquer algorithm use to study some benzenoid hydrocarbons. A graphtheoretic and computational approach

A computer program based on a divide-and-conquer algorithm was used to numerically split a univariate-polynomial into factors depicting the various parts of E-pi (pi: electronic energy) and K (total Kekule structure count) of the benzenoid graphs. A multivariate regression equation is suggested, taking n, m, and K-i as the independent variables and E-pi (total) as the dependent variable; n, m, and K-i are the number of vertices, edges, and the fraction of the total K, respectively. A satisfactory correlation coefficient (R-2 > 0.99) was obtained

A novel use of Hückel parameters (h, k) for the pairing of eigenvalues in graph spectrum

813-817An unusual use of the Hückel parameters (h and k) has been noticed for the derivation of the characteristic polynomial (CP) of the vertex-edge weighted graphs. A new pairing scheme for the eigenvalues (xj) of the weighed graphs has been proposed in the light of Coulson-Rushbrooke pairing theorem for the non-bipartite graphs, xj + xn+ 1-j = 1/2 hp ± a for j = 1, 2, 3 ..., n where n, p and ‘a’ are the number of vertices, number of heteroatoms and a numerical quantity respectively

Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of and toxin nanopores in lipid membranes

Pore forming toxins (PFTs) are virulent proteins whose primary goal is to lyse target cells by unregulated pore formation. Molecular dynamics simulations can potentially provide molecular insights on the properties of the pore complex as well as the underlying pathways for pore formation. In this manuscript we compare both coarse-grained (MARTINI force-field) and all-atom simulations, and comment on the accuracy of the MARTINI coarse-grained method for simulating these large membrane protein pore complexes. We report 20 long coarse-grained MARTINI simulations of prototypical pores from two different classes of pore forming toxins (PFTs) in lipid membranes - Cytolysin A (ClyA), which is an example of an toxin, and -hemolysin (AHL) which is an example of a toxin. We compare and contrast structural attributes such as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from the MARTINI simulations with all-atom simulations. RMSD histograms sampled by the MARTINI simulations are about a factor of 2 larger, and the radius profiles show that the transmembrane domains of both ClyA and AHL pores undergo significant distortions, when compared with the all-atom simulations. In addition to the fully inserted transmembrane pores, membrane-inserted proteo-lipid ClyA arcs show large shape distortions with a tendency to close in the MARTINI simulations. While this phenomenon could be biologically plausible given the fact that -toxins can form pores of varying sizes, the additional flexibility is probably due to weaker inter-protomer interactions which are modulated by the elastic dynamic network in the MARTINI force-field. We conclude that there is further scope for refining inter-protomer contacts and perhaps membrane-protein interactions in the MARTINI coarse-grained framework. A robust coarse-grained force-field will enable one to reliably carry out mesoscopic simulations which are required to understand protomer oligomerization, pore formation and leakage

Differential dynamics of the serotonin_1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation

<p>The serotonin_1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin_1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin_1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin_1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.</p