Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC VIVE and the OCULUS RIFT utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

'Something in the way she moves': The functional significance of flexibility in the multiple roles of protein disulfide isomerase (PDI).

Protein disulfide isomerase (PDI) has diverse functions in the endoplasmic reticulum as catalyst of redox transfer, disulfide isomerization and oxidative protein folding, as molecular chaperone and in multi-subunit complexes. It interacts with an extraordinarily wide range of substrate and partner proteins, but there is only limited structural information on these interactions. Extensive evidence on the flexibility of PDI in solution is not matched by any detailed picture of the scope of its motion. A new rapid method for simulating the motion of large proteins provides detailed molecular trajectories for PDI demonstrating extensive changes in the relative orientation of its four domains, great variation in the distances between key sites and internal motion within the core ligand-binding domain. The review shows that these simulations are consistent with experimental evidence and provide insight into the functional capabilities conferred by the extensive flexible motion of PDI.

The flexibility and dynamics of protein disulfide isomerase.

We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse-graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures-and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776-1785. © 2016 Wiley Periodicals, Inc.

Characterization of folding cores in the cyclophilin A-cyclosporin A complex.

Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids that make up the folding core include hydrogen-deuterium exchange and Φ-value analysis and can be expensive and time consuming. Because of this, there is a desire to improve upon existing methods for determining protein folding cores theoretically. We have obtained HDX data for the complex of cyclophilin A with the immunosuppressant cyclosporin A. We compare these data, as well as literature values for uncomplexed cyclophilin A, to theoretical predictions using a combination of rigidity analysis and coarse-grained simulations of protein motion. We find that in this case, the most specific prediction of folding cores comes from a combined approach that models the rigidity of the protein using the first software suite and the dynamics of the protein using the froda tool.

Flexibility and mobility of SARS-CoV-2-related protein structures.

The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein-using its complete homo-trimer configuration with 2905 residues-our method identifies a large-scale opening and closing of the S1 subunit through movement of the S[Formula: see text] domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.

Critical parameters from a generalized multifractal analysis at the Anderson transition.

We propose a generalization of multifractal analysis that is applicable to the critical regime of the Anderson localization-delocalization transition. The approach reveals that the behavior of the probability distribution of wave function amplitudes is sufficient to characterize the transition. In combination with finite-size scaling, this formalism permits the critical parameters to be estimated without the need for conductance or other transport measurements. Applying this method to high-precision data for wave function statistics obtained by exact diagonalization of the three-dimensional Anderson model, we estimate the critical exponent ν=1.58±0.03.

Spin-polarized localization in a magnetized chain.

We investigate a simple tight-binding Hamiltonian to understand the stability of spin-polarized transport of states with an arbitrary spin content in the presence of disorder. The general spin state is made to pass through a linear chain of magnetic atoms, and the localization lengths are computed. Depending on the value of spin, the chain of magnetic atoms unravels a hidden transverse dimensionality that can be exploited to engineer energy regimes where only a selected spin state is allowed to retain large localization lengths. We carry out a numerical anmalysis to understand the roles played by the spin projections in different energy regimes of the spectrum. For this purpose, we introduce a new measure, dubbed spin-resolved localization length. We study uncorrelated disorder in the potential profile offered by the magnetic substrate or in the orientations of the magnetic moments concerning a given direction in space. Our results show that the spin filtering effect is robust against weak disorder and hence the proposed system should be a good candidate model for experimental realizations of spin-selective transport devices.

A type of robust superlattice type-I Weyl semimetal with four Weyl nodes.

We investigate the topological properties of the Janus superlattices WTeS and WTeSe by first-principles methods and Wannier-based tight-binding Hamiltonians. The thermal stability of the Janus structures is checked by first-principles molecular dynamics. The topological properties are identified through node chirality, surface states and surface Fermi arcs. Our calculations reveal that both WTeS and WTeSe are Type-I Weyl semimetals with only four Weyl nodes in the Brillouin zone, which is a minimal number in a time reversal symmetry system. This small number of Weyl nodes makes them an excellent platform to study their topological properties experimentally. The Weyl nodes are located in four different quadrants of the Brillouin zone and consequently the separation of Weyl points in reciprocal space, and the length of Fermi arc, is of the order of the magnitude of the reciprocal lattice vector |Gz| as might be easily observed in experiment. The Weyl nodes have approximately the same energy below the Fermi level and are hence accessible by conventional ARPES. In addition, under external strain, the Weyl semimetal state is more robust than the sister compounds Td-WTe2/MoTe2. Our findings are important to explore Weyl fermion physics and useful for realizing possible applications of Weyl semimetal materials in future topological electronic devices.

Spin filter for arbitrary spins by substrate engineering.

We design spin filters for particles with potentially arbitrary spin [Formula: see text] using a one-dimensional periodic chain of magnetic atoms as a quantum device. Describing the system within a tight-binding formalism we present an analytical method to unravel the analogy between a one-dimensional magnetic chain and a multi-strand ladder network. This analogy is crucial, and is subsequently exploited to engineer gaps in the energy spectrum by an appropriate choice of the magnetic substrate. We obtain an exact correlation between the magnitude of the spin of the incoming beam of particles and the magnetic moment of the substrate atoms in the chain desired for opening up of a spectral gap. Results of spin polarized transport, calculated within a transfer matrix formalism, are presented for particles having half-integer as well as higher spin states. We find that the chain can be made to act as a quantum device which opens a transmission window only for selected spin components over certain ranges of the Fermi energy, blocking them in the remaining part of the spectrum. The results appear to be robust even when the choice of the substrate atoms deviates substantially from the ideal situation, as verified by extending the ideas to the case of a 'spin spiral'. Interestingly, the spin spiral geometry, apart from exhibiting the filtering effect, is also seen to act as a device flipping spins-an effect that can be monitored by an interplay of the system size and the period of the spiral. Our scheme is applicable to ultracold quantum gases, and might inspire future experiments in this direction.

Leaf-to-leaf distances and their moments in finite and infinite ordered m-ary tree graphs.

We study the leaf-to-leaf distances on one-dimensionally ordered, full and complete m-ary tree graphs using a recursive approach. In our formulation, unlike in traditional graph theory approaches, leaves are ordered along a line emulating a one-dimensional lattice. We find explicit analytical formulas for the sum of all paths for arbitrary leaf separation r as well as the average distances and the moments thereof. We show that the resulting explicit expressions can be recast in terms of Hurwitz-Lerch transcendants. Results for periodic trees are also given. For incomplete random binary trees, we provide first results by numerical techniques; we find a rapid drop of leaf-to-leaf distances for large r.

Numerical study of eigenvector statistics for random banded matrices.

The statistics of eigenvector amplitudes near the band center in random-banded-matrix ensembles is studied numerically. The nonlinear sigma model provides a rigorous description of the statistics in these ensembles. We are interested in the extension of the predictions of the sigma model approach to complex quantum systems. We study the validity range of the perturbation theory beginning from the well-known formulas in random matrix theory.

Protein flexibility is key to cisplatin crosslinking in calmodulin.

Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and protein-protein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the inter-residue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca4-CaM). The possibility of cisplatin crosslinking Ca4-CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca4-CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs.

The interplay of mutations and electronic properties in disease-related genes.

Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as p53 by detection of oxidative damage. However, the reproducible measurement and modelling of charge migration through DNA molecules at the nanometer scale remains a challenging and controversial subject even after more than a decade of intense efforts. Here we show, by analysing 162 disease-related genes from a variety of medical databases with a total of almost 20,000 observed pathogenic mutations, a significant difference in the electronic properties of the population of observed mutations compared to the set of all possible mutations. Our results have implications for the role of the electronic properties of DNA in cellular processes, and hint at the possibility of prediction, early diagnosis and detection of mutation hotspots.

Multifractal analysis with the probability density function at the three-dimensional anderson transition.

The probability density function (PDF) for critical wave function amplitudes is studied in the three-dimensional Anderson model. We present a formal expression between the PDF and the multifractal spectrum f(alpha) in which the role of finite-size corrections is properly analyzed. We show the non-Gaussian nature and the existence of a symmetry relation in the PDF. From the PDF, we extract information about f(alpha) at criticality such as the presence of negative fractal dimensions and the possible existence of termination points. A PDF-based multifractal analysis is shown to be a valid alternative to the standard approach based on the scaling of inverse participation ratios.

Exciton storage in a nanoscale Aharonov-Bohm ring with electric field tuning.

We study analytically the optical properties of a simple model for an electron-hole pair on a ring subjected to perpendicular magnetic flux and in-plane electric field. We show how to tune this excitonic system from optically active to optically dark as a function of these external fields. Our results offer a simple mechanism for exciton storage and readout.

Point-mutation effects on charge-transport properties of the tumor-suppressor gene p53.

We report on a theoretical study of point mutations effects on charge transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On the basis of effective tight-binding models which simulate hole propagation along the DNA, a statistical analysis of mutation-induced charge transfer modifications is performed. In contrast to noncancerous mutations, mutation hot spots tend to result in significantly weaker changes of transmission properties. This suggests that charge transport could play a significant role for DNA-repairing deficiency yielding carcinogenesis.

Electronic transport in DNA.

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and lambda-DNA. We find that random and lambda-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA.