Unique Flexibility Patterns of PDB Entries

Sunday, February 28, 2016 find that while the two anomers induce similar RBD-RBD reorientations, they produce strikingly different conformational ensemble shifts within individual RBDs, suggesting that allosteric signaling must involve the RBD-FAD interface. Further analysis yields a cluster of residues proximal to both RBDFAD and RBD-RBD interfaces whose conformational ensembles are shifted by a-sialic acid. Together, these results suggest that allosteric coupling between RBD and FAD involves a complex pathway comprising of multiple interdomain interfaces. 276-Pos Board B56 Molecular Insights for the Role of Key Residues of Calreticulin in its Binding Activities Hongyi Yang, Joanne E. Murphy-Ullrich, Yuhua Song. Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, USA. Calreticulin (CRT) is localized to and has functions in multiple cellular compartments, including cell surface, endoplasmic reticulum, and extracellular matrix (FASEB J. 24: 665- 683, 2010). Mutagenesis studies have identified several residues on a concave b-sheet surface of CRT critical for CRT binding to carbohydrate and other proteins/peptides (J. Biol. Chem. 285: 38612-20, 2010). How the mutations of these key residues in CRT affect the conformation and dynamical motion of CRT, further influencing CRT binding activities remain unknown. In this study, we investigated the effect of several key point mutations on the conformational and dynamical motion changes of CRT via atomistic molecular dynamics simulations. The CRT structure is obtained based on the crystal structure of the globular lectin domain and partial P-domain of CRT, and the NMR structure of P-domain (flexible arm domain). Results from this study show that the mutations of the key residues of CRT result in the changes in the protein’s local backbone flexibility and some of the point mutations cause significant changes of the relatively position and orientation between the CRT lectin and P-domains. Within the b-strands in CRT’s lection domain, mutant-induced secondary structural changes, including the changes in the residues of b-strand occupancy, number of H-bonds and hydrophobic contacts, are observed. The mutations of the key residues on the concave b-sheet surface of CRT also result in the changes of the solvent accessible surface area, side-chain relative positions and dynamical correlated motions, which could directly affect CRT binding activities. Results from this study provided molecular insight into the effect of the mutations of key residues of CRT on CRT conformational and dynamical motion changes, further influencing CRT binding to carbohydrates and other proteins to signal the important cellular activities. 277-Pos Board B57 Unique Flexibility Patterns of PDB Entries Monique M. Tirion. Physics, Clarkson University, Potsdam, NY, USA. Solid bodies obtain characteristic mass and charge distributions, principle rotational axes as well as internal symmetry axes. Internal symmetry axes are uniquely identified by Normal Mode Analysis (NMA) and are widely used in the fields of engineering and seismology to model the redistribution of modest energy influxes into non-rigid bodies. NMA of protein systems rapidly and reproduceably identify their internal flexibility characteristics. Protein systems typically consist of thousands of atoms and three times as many Cartesian degrees of freedom (dofs). These systems can equally well be characterized by their internal dofs: bond lengths, bond angles and bond rotations. Small energy perturbations like thermal baths primarily activate bond-rotations or dihedrals. Use of dihedral dofs ensures that bond lengths and bond angles remain stereochemically sound. We have shown that use of these dofs combined with distance- and atom-dependent Hookian potentials correctly reproduce theoretical dispersion spectra. Use of linearized potentials permits NMA of PDB coordinates: No initial, structure-distorting energy minimization is required. This feature permits analyses of PDB structures that differ only slightly such as (i) two isoforms of the same X-ray electron density, (ii) the same structure solved in two different crystal forms, or (iii) two evolutionary related proteins that share high structural, not sequence, homology. We examine the modal signatures of several cases and report meaningful differences. In one, glycoside hydrolase family 10 xylanases, the A and B isoforms of the same crystal place three out of 302 residues in alternate conformations. Their modal analyses reveal significant differences in their slowest modes, consistent with predictions that GH-10 members consist of two subgroups with differing mobility. In another, the modal analysis of two closely related tertiary structures with low sequence homology, lactadherin and Factor VIII glycoprotein, reveal significant differences consistent with H/D exchange data.

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278-Pos Board B58 Loss in Allosteric Regulations through Structural Dynamics Lead to Disease Avishek Kumar, Tyler J. Glembo, Banu Ozkan. Physics, Arizona State University, Tempe, AZ, USA. Determining the three-dimensional structure of myoglobin, the first solved structure of a protein, fundamentally changed the way protein function was understood. Even more revolutionary was the information that came afterward: structure encoded protein dynamics underlies biological functions. In protein evolution, the classical view of the one sequence-one structure-one function paradigm is now being extended to a new view: an ensemble of conformations in equilibrium that can evolve new functions. Therefore, understanding structural dynamics is crucial to obtaining a more complete picture of protein evolution. We recently analyzed the evolution of different protein families including GFP proteins, beta-lactamase inhibitors, and nuclear receptors. Using Molecular Dynamics to compute the equilibrium dynamics and quantifying the contribution of each residue to the dynamics through the Dynamic Flexibility Index (DFI), we have observed that the alteration of conformational dynamics through allosteric regulation leads to functional changes. Moreover, our proteome-wide conformational dynamics analysis of over 100 human proteins shows that mutations occurring at rigid residue positions are more susceptible to disease. Analysis of the wild type light chain subunit of human ferritin protein along with the neutral and disease forms reveal that disease-associated mutations may impair dynamic allosteric regulations leading to a loss of function. Indeed, neutral variants and the wild type exhibit similar DFI profiles in which experimentally determined functionally critical sites act as hinges in controlling the overall motion. On the other hand, disease mutations make hinges more loose (i.e., softens the hinges),impairing the allosterically regulated dynamics 279-Pos Board B59 Universality of Vibrational Spectra of Globular Proteins Hyuntae Na1, Guang Song1, Daniel ben-Avraham2. 1 Computer Science, Iowa State University, Ames, IA, USA, 2Physics, Clarkson University, Potsdam, NY, USA. The density of frequencies of the vibrational spectrum of proteins is the focus of much interest, as it is quite readily available experimentally, and a prerequisite for the theoretical computation of several physical properties of the proteins. Here we show that the vibrational spectrum density of globular proteins is universal, that is, it closely follows one universal curve regardless of the fold, size and other details of the protein in question. While previous claims of universality relied on but a few proteins and on normal modes analyses (NMA) restricted to only torsional degrees of freedom and to the low-frequency range of 0 - 300 1/cm, our present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, finds that universality holds for all frequencies (up to 4000 1/cm), where seemingly idiosyncratic peaks and turns in the density of states are faithfully reproduced from one protein to the next. We characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such ‘‘outlier’’ proteins. The method used for the derivation of the vibrational modes (potential energy formulation and parameterization, set of degrees of freedom employed, etc.) is found to have a dramatic effect on the spectral density, so that universality can provide an exquisite tool for assessing and improving the quality of various theoretical models used for NMA computations. Finally, we show that the input configuration of the proteins affects the density of modes as well, thus emphasizing the importance of simplified potential energy formulations that are minimized at the outset, at the protein’s given configuration. 280-Pos Board B60 The Degeneracy of Protein Normal Modes Hyuntae Na, Guang Song. Computer Science, Iowa State University, Ames, IA, USA. Normal modes are frequently computed and used to portray protein dynamics and interpret conformation changes that take place during functional processes. In this work, we investigate the nature of normal modes and find that the normal modes of proteins, especially those at the low frequency range, are degenerated. The degeneracy of a mode means a mode mixes with other modes with similar frequency and vanishes under slight structural uncertainty. This work is built upon our recent discovery that the vibrational spectrum of globular proteins is universal. The high density of modes as shown in the vibrational frequency spectrum renders protein normal modes highly degeneratable, under even smallest structure uncertainty that unavoid-