Efficient minimization of multipole electrostatic potentials in torsion space

The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom

PocketPicker: analysis of ligand binding-sites with shape descriptors

Background Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design. Characterizing the active site's shape as well as the distribution of surrounding residues plays an important role for a variety of applications such as automated ligand docking or in situ modeling. Comparing the shape similarity of binding site geometries of related proteins provides further insights into the mechanisms of ligand binding. Results We present PocketPicker, an automated grid-based technique for the prediction of protein binding pockets that specifies the shape of a potential binding-site with regard to its buriedness. The method was applied to a representative set of protein-ligand complexes and their corresponding apo-protein structures to evaluate the quality of binding-site predictions. The performance of the pocket detection routine was compared to results achieved with the existing methods CAST, LIGSITE, LIGSITEcs, PASS and SURFNET. Success rates PocketPicker were comparable to those of LIGSITEcs and outperformed the other tools. We introduce a descriptor that translates the arrangement of grid points delineating a detected binding-site into a correlation vector. We show that this shape descriptor is suited for comparative analyses of similar binding-site geometry by examining induced-fit phenomena in aldose reductase. This new method uses information derived from calculations of the buriedness of potential binding-sites. Conclusions The pocket prediction routine of PocketPicker is a useful tool for identification of potential protein binding-pockets. It produces a convenient representation of binding-site shapes including an intuitive description of their accessibility. The shape-descriptor for automated classification of binding-site geometries can be used as an additional tool complementing elaborate manual inspections

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2–4% depending on the grid resolution, which is 1.5–4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf

ATOMISTIC SIMULATIONS OF INTRINSICALLY DISORDERED PROTEIN FOLDING AND DYNAMICS

Intrinsically disordered proteins (IDPs) are crucial in biology and human diseases, necessitating a comprehensive understanding of their structure, dynamics, and interactions. Atomistic simulations have emerged as a key tool for unraveling the molecular intricacies and establishing mechanistic insights into how these proteins facilitate diverse biological functions. However, achieving accurate simulations requires both an appropriate protein force field capable of describing the energy landscape of functionally relevant IDP conformations and sufficient conformational sampling to capture the free energy landscape of IDP dynamics. These factors are fundamental in comprehending potential IDP structures, dynamics, and interactions. I first conducted explicit solvent simulations to assess the performance of two state-of-the-art protein force fields, namely CHARMM36m and a99SB-disp, in capturing the stability of small protein-protein interactions. To evaluate their accuracy, I selected a set of 46 amino acid backbone and side chain pairs with representative configurations and computed the free energy profiles of their interactions. The results demonstrated that CHARMM36m consistently predicted stronger protein-protein interactions compared to a99SB-disp. Notably, the most significant overestimation in CHARMM36m occurred in charged pairs involving Arg and Glu side chains, with an overestimation of up to 2.9 kcal/mol. Through free energy decomposition analysis, I determined that these overestimations were primarily driven by protein-water electrostatic interactions rather than van der Waals (vdW) interactions. Consequently, these findings suggest that careful rebalancing of electrostatic interactions should be considered in the further optimization of protein force fields. In order to enhance the conformational sampling of IDPs, I developed an integrated approach that combines an improved implicit solvent model called Generalized Born with molecular volume and solvent accessible surface area (GBMV2/SA) with a multiscale enhanced sampling (MSES) technique. To make this approach more efficient, I implemented it as a standalone OpenMM plugin on Graphics Processing Units (GPUs). The results demonstrated that the GPU-GBMV2/SA model achieved numerical equivalence to the original CPU-GBMV2/SA models, while providing a remarkable ~60x speedup on a single NVIDIA TITAN X (Pascal) graphics card for molecular dynamic simulations of both folded and unstructured proteins. This significant acceleration greatly facilitated the application of the approach in biomolecular simulations. In addition, I conducted an evaluation of the reliability of GBMV2/SA models in simulating both folded and unfolded proteins. The results revealed that the GBMV2/SA model accurately describes small proteins, but its applicability is limited when it comes to larger proteins such as KID and p53-TAD proteins. This limitation can be attributed to the absence of long-range solute-solvent dispersion interactions in the model. To address this issue, I introduced a comprehensive treatment of nonpolar solvation free energy called GBMV2/NP model. Unfortunately, the GBMV2/NP model exhibited a destabilizing effect on well-folded proteins, particularly larger ones, due to an inaccurate representation of the repulsive solvent accessible surface area (SASA) model caused by the utilization of unphysical van der Waals volume. This observation highlights the need for further improvements in accurately describing the nonpolar term in the model

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

Diazaborole Linked Porous Polymers: Design, Synthesis, and Application to Gas Storage and Separation

The synthesis of highly porous organic polymers with predefined porosity has attracted considerable attention due to their potential in a wide range of applications. Porous organic polymers (POPs) offer novel properties such as permanent porosity, adjustable chemical nature, and noteworthy thermal and chemical stability. These remarkable properties of the POPs make them promising candidates for use in gas separation and storage. The emission of carbon dioxide (CO2) from fossil fuel combustion is a major cause of global warming. Finding an efficient separation and/or storage material is essential for creating a cleaner environment. Therefore, the importance of the POPs in the field is undeniable. Along these pursuits, several porous polymers have been synthesized with different specifications. The first class of porous polymers are called Covalent Organic Frameworks (COFs). They possess highly ordered structures with very high surface areas and contain light elements. COFs based on B-O, C-N, and B-N bonds have been reported so far. In particular, COFs based on B-O bond formation are well investigated due to the kinetically labile nature of this bond which is essential for overcoming the crystallization problem of covalent networks. Along this line, triptycene-derived covalent organic framework (TDCOF-5) has been synthesized through a condensation reaction between 1, 4-benzenediboronic acid and hexahydroxytriptycene which leads to the formation of boronate ester linkage. TDCOF-5 has the highest H2 uptake under 1 atm at 77K (1.6%) among all known 2D and 3D COFs derived from B–O bond formation and moderate CO2 uptake (2.1 mmol g-1) with Qst values of 6.6 kJ mol-1 and 21.8 kJ mol-1, respectively. The second class of porous structures discussed herein is diazaborole linked polymers (DBLPs). They are constructed based on B-N bond formation and possess amorphous structures due to the lack of the reversible bond formation processes. At this scope, 2, 3, 6, 7, 14, 15-hexaaminotriptycene (HATT) hexahydrocloride was synthesized and reacted with different boronic acid derivatives to produce three different porous polymers under condensation reaction conditions. DBLP-3, -4 and -5 have very high surface areas; 730, 904, and 986 m2 g-1, and offer high CO2 uptake (158.5, 198, and 171.5 mg g-1) at 1 bar and 273 K, respectively. DBLPs have much higher CO2 uptake capacity when compared to almost all reported B-N and B-O containing porous polymers in the field. In addition to high CO2 capacity, DBLPs showed remarkable CO2/N2 and CO2/CH4 selectivity, when the Henry`s law of initial slope selectivity calculations were applied. In general, DBILPs exhibit high selectivities for CO2/N2 (35-51) and CO2/CH4 (5-6) at 298 K which are comparable to those of most porous polymers

New Synthetic Strategies for Improved Gas separation by Nanoporous Organic Polymers

Abstract NEW SYNTHETIC STRATEGIES FOR IMPROVED GAS SEPARATION BY NANOPOROUS ORGANIC POLYMERS Suha S. Altarawneh, Ph.D. The emission of carbon dioxide (CO2) from fossil fuel combustion is a major cause of climate change. Therefore, the efficient separation of CO2 from mixtures of gases such as flue gas and impure sources of CH4 (e.g. natural gas and landfill gas) is an essential step in meeting the ever increasing demands on natural gas and creating a cleaner environment. Carbon capture and storage technology (CCS) is one of the methods employed for gas separation using chemisorption and/or physisorption processes. Several materials such as porous polymers and amine solutions have been used as gas adsorbents. However, the amount of energy required for the adsorbent regeneration is one of the main concerns that needs to be addressed. In this regard, porous organic polymers (POPs) with defined porosity and preferential binding affinity for CO2 over N2 and CH4 are some of the most attractive materials that could fulfill the above requirement and are also applicable for use in gas storage and separation. Suitable POPs that can be used for gas storage applications need to have high porosity and mechanical stability under high pressure conditions (~100 bar). Alternatively, the most effective POPs in gas separation are those that have preferential binding affinity for CO2 over other gases present at low pressure settings. In all cases, the chemical nature of POPs and their textural properties are key parameters, however, the modest surface area of most POPs limits their efficiency. With the above considerations in mind, the aim of our research is to develop benzimidazole–linked polymers (BILPs) that have variable porosity levels and chemical functionality to enhance gas separation (CO2/CH4, CO2/N2). We have established new synthetic routes that utilize polycondensation reactions between aryl-aldehydes and aryl-o-diamine building units to construct new BILPs with improved gas separation properties. Our strategy targeted structural and textural modifications of BILPs. We used longer linkers (building units) to improve porosity; however, the flexible linkers offered only low porosity due to network interpenetration. To overcome this challenge, a more controlled network growth rate was assessed by adjusting imine-bond formation rates through different acid loading. The acid, HCl, was used to catalyze imine-bond formation. The new resulting acid-catalyzed BILPs have shown an improved porosity up to 92% compared to the non-catalyzed BILPs. We also used the “rational ligand design” approach to introduce new functionalities into BILPs (-OR) to alter the hydrophobic nature of their pores. In this regard, we have illustrated the applicability of this strategy to BILPs containing flexible aryl-o-diamine linkers. The bulky alkoxy groups were incorporated into the aryl-aldehyde building unit prior to polymerization. The resulting polymers have proven that the presence of the bulky pendant alkoxy-chains plays a significant role during the polymerization process which allows for increased control over network formation, and in turn, porosity. Sorption measurements, selectivity, and heats of adsorption data have confirmed the positive impact of the alkoxy-groups and shown that varying the pendant groups is a promising method for designing highly porous BILPs. In addition to pore functionalization with alkoxy-chains, we used pi-conjugated and N-rich building units to prepare new BILPs that have semiconducting properties in addition to their porous nature. This class of BILPs has shown that the extended-conjugated system improved BILPs electronic properties. The other studies performed in this research, involved the use of DFT theory to investigate CO2/BILPs interaction sites and binding affinities. The computational outcomes of DFT have shown that (C-H) bond of the aryl system is a possible site for CO2 interaction beside the free-N side and hydrogen bonding. All new polymers were characterized by spectral and analytical characterization methods and their sorption data were collected to evaluate their capability as candidates for gas separation applications