Optimization of parameters of nonbonded interactions in a spectroscopically determined force field

A procedure is given by which parameters of nonbonded interactions in a molecular mechanics energy function can be optimized for maximum compatibility with ab initio force fields and structures. The method is based on a previously derived transformation of ab initio valence parameters to the molecular mechanics formalism. Explicit analytical expressions for the derivatives of the molecular mechanics force constants and reference geometry parameters with respect to the parameters of the nonbonded interactions are derived. The form of the goodness-of-fit function is discussed. A first application to a set of alanine dipeptides is described.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30924/1/0000594.pd

Potential energy functions: From consistent force fields to spectroscopically determined polarizable force fields

We review our methodology for producing physically accurate potential energy functions, particularly relevant in the context of Lifson's goal of including frequency agreement as one of the criteria of a self-consistent force field. Our spectroscopically determined force field (SDFF) procedure guarantees such agreement by imposing it as an initial constraint on parameter optimization, and accomplishes this by an analytical transformation of ab initio “data” into the energy function format. After describing the elements of the SDFF protocol, we indicate its implementation to date and then discuss recent advances in our representation of the force field, in particular those required to produce an SDFF for the peptide group. © 2003 Wiley Periodicals, Inc. Biopolymers: 383–394, 2003Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34327/1/10254_ftp.pd

Valence Force Fields as a Tool in Vibrational Spectroscopy and Molecular Mechanics

Force field calculations on conjugated molecules are discussed. The discussion is based on the experience of a series of overlay calculations, recently carried out, where the transferability of force constants was thoroughly studied. Successful applications as well as limitations of the constructed force field are described. The effects of nonbonded interactions are recognized as the most serious restriction of the transferability of valence force fields, and it is suggested that the molecular mechanics method, where the nonbonded interactions are taken explicitly into account, would be advantageous. The treatment of potential energy in the molecular mechanics method is briefly described and theconnections between valence force constants and potential energy parameters in this method are discussed

A polarizable electrostatic model of the N-methylacetamide dimer

Our previously developed polarizable electrostatic model is applied to isolated N-methylacetamide (NMA) and to three hydrogen-bonded configurations of the NMA dimer. Two versions of the model are studied. In the first one (POL1), polarizability along the valence bonds is described by induced bond charge increments, and polarizability perpendicular to the bonds is described by cylindrically isotropic induced atomic dipoles. In the other version (POL2), the induced bond charge increments are replaced by induced atomic dipoles along the bonds. The parameterization is done by fitting to ab initio MP2/6-31++G(d,p) electric potentials. The polarizability parameters are determined by subjecting the NMA molecule to various external electric fields. POL1 turns out to be easier to optimize than POL2. Both models reproduce well the ab initio electric potentials, molecular dipole moments, and molecular polarizability tensors of the monomer and the dimers. Nonpolarizable models are also investigated. The results show that polarization is very important for reproducing the electric potentials of the studied dimers, indicating that this is also the case in hydrogen bonding between peptide groups in proteins. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1933–1943, 2001Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34694/1/1143_ftp.pd

pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

Nitrophorins are NO carrier proteins that transport and release NO through a pH-dependent conformational change. They bind NO tightly in a low pH environment and release it in a higher pH environment. Experimental evidence shows that the increase in the NO dissociation equilibrium constant, K d, is due mainly to an increase in the NO release rate. Structural and kinetic data strongly suggest that NPs control NO escape by modulating its migration from the active site to the solvent through a pH-dependent conformational change. NP2 and NP4 are two representative proteins of the family displaying a 39% overall sequence identity, and interestingly, NP2 releases NO slower than NP4. The proposal that NPs' NO release relies mainly on the NO escape rate makes NPs a very peculiar case among typical heme proteins. The connection between the pH-dependent conformational change and ligand release mechanism is not fully understood and the structural basis for the pH induced structural transition and the different NO release patterns in NPs are unresolved, yet interesting issues. In this work, we have used state of the art molecular dynamics simulations to study the NO escape process in NP2 and NP4 in both the low and high pH states. Our results show that both NPs modulate NO release by switching between a "closed" conformation in a low pH environment and an "open" conformation at higher pH. In both proteins, the change is caused by the differential protonation of a common residue Asp30 in NP4 and Asp29 in NP2, and the NO escape route is conserved. Finally, our results show that, in NP2, the conformational change to the "open" conformation is smaller than that for NP4 which results in a higher barrier for NO release.Fil: Swails, Jason M.. University of Florida; Estados UnidosFil: Meng, Yilin. University of Florida; Estados UnidosFil: Walker, F. Ann. University of Arizona; Estados UnidosFil: Marti, Marcelo Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados Unido

Developing and validating Fuzzy-Border continuum solvation model with POlarizable Simulations Second order Interaction Model (POSSIM) force field for proteins

The accurate, fast and low cost computational tools are indispensable for studying the structure and dynamics of biological macromolecules in aqueous solution. The goal of this thesis is development and validation of continuum Fuzzy-Border (FB) solvation model to work with the Polarizable Simulations Second-order Interaction Model (POSSIM) force field for proteins developed by Professor G A Kaminski. The implicit FB model has advantages over the popularly used Poisson Boltzmann (PB) solvation model. The FB continuum model attenuates the noise and convergence issues commonly present in numerical treatments of the PB model by employing fixed position cubic grid to compute interactions. It also uses either second or first-order approximation for the solvent polarization which is similar to the second-order explicit polarization applied in POSSIM force field. The FB model was first developed and parameterized with nonpolarizable OPLS-AA force field for small molecules which are not only important in themselves but also building blocks of proteins and peptide side chains. The hydration parameters are fitted to reproduce the experimental or quantum mechanical hydration energies of the molecules with the overall average unsigned error of ca. 0.076kcal/mol. It was further validated by computing the absolute pKa values of 11 substituted phenols with the average unsigned error of 0.41pH units in comparison with the quantum mechanical error of 0.38pH units for this set of molecules. There was a good transferability of hydration parameters and the results were produced only with fitting of the specific atoms to the hydration energy and pKa targets. This clearly demonstrates the numerical and physical basis of the model is good enough and with proper fitting can reproduce the acidity constants for other systems as well. After the successful development of FB model with the fixed charges OPLS-AA force field, it was expanded to permit simulations with Polarizable Simulations Second-order Interaction Model (POSSIM) force field. The hydration parameters of the small molecules representing analogues of protein side chains were fitted to their solvation energies at 298.15K with an average error of ca.0.136kcal/mol. Second, the resulting parameters were used to reproduce the pKa values of the reference systems and the carboxylic (Asp7, Glu10, Glu19, Asp27 and Glu43) and basic residues (Lys13, Lys29, Lys34, His52 and Lys55) of the turkey ovomucoid third domain (OMTKY3) protein. The overall average unsigned error in the pKa values of the acid residues was found to be 0.37pH units and the basic residues was 0.38 pH units compared to 0.58pH units and 0.72 pH units calculated previously using polarizable force field (PFF) and Poisson Boltzmann formalism (PBF) continuum solvation model. These results are produced with fitting of specific atoms of the reference systems and carboxylic and basic residues of the OMTKY3 protein. Since FB model has produced improved pKa shifts of carboxylic residues and basic protein residues in OMTKY3 protein compared to PBF/PFF, it suggests the methodology of first-order FB continuum solvation model works well in such calculations. In this study the importance of explicit treatment of the electrostatic polarization in calculating pKa of both acid and basic protein residues is also emphasized. Moreover, the presented results demonstrate not only the consistently good degree of accuracy of protein pKa calculations with the second-degree POSSIM approximation of the polarizable calculations and the first-order approximation used in the Fuzzy-Border model for the continuum solvation energy, but also a high degree of transferability of both the POSSIM and continuum solvent Fuzzy Border parameters. Therefore, the FB model of solvation combined with the POSSIM force field can be successfully applied to study the protein and protein-ligand systems in water

Accuracy of quantum mechanically derived force-fields parameterized from dispersion-corrected DFT data: the benzene dimer as a prototype for aromatic interactions

A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure (Cacelli et al. J. Comput. Chem. 2012, 33, 1055) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions

Atomistic simulations of the reactive processes in the heme-containing proteins

Heme proteins have a great impact in the protein research. Due to the unique electronic properties of heme these proteins are abundant in nature and have a wide range of biological functions in most of the organisms from archea to eukaryotes. The ability of heme proteins to bind and release small molecules like CO, NO, O2 defines the variety of physiological functions and is related to the structural dynamic properties of the protein matrix surrounding heme. Cytochrome c oxidase (CcO) is a heme-containing protein, which performs oxygen reduction to water as a part of the membrane complex. Cytochrome c oxidase forms a stable complex with CO in the binuclear heme a3 - Cu(B) active site and is a model system to study ligand binding and release. The pump-probe experiments performed for the CcO-CO system reported the ultrafast dynamics of the CO transfer from the heme Fe to Cu(B) site. Molecular dynamics simulations are used to provide the dynamic structural information during the transfer with atomic resolution. The kinetics of the process determined from the MD simulations is a qualitative agreement with the timescales reported in the experimental studies. The simulations show that the transfer dynamics is ballistic. The doming of the heme Fe observed after the photoexcitation significantly affects the probability of the heme Fe rebinding. Myglobin (Mb) is an oxygen storage protein, the active site of which contains heme. It allows studying the impact of the structural changes on binding and release of small molecules. The Mb complex with NO was studied using MD simulations. The heme doming effect observed after photodissociation makes the heme Fe less accessible to NO and slows down the rebinding. The DFT parametrized 2A state predicts the existence of the Fe-ON minimum, which is not observable in the experiments, this might be explained by the effect of the 4A PES, that activated during the photoexcitation and that has a lower energy for the configurations corresponding to the Fe-ON minimum