Papers by Michael Schnieders
The Journal of Chemical Physics, 2006
Molecular dynamics simulations were performed using a modified amoeba force field to determine hy... more Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca 2+ and Mg 2+ . The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Tholé polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.
PDZD7 and hearing loss: More than just a modifier
American journal of medical genetics. Part A, Jan 29, 2015
Deafness is the most frequent sensory disorder. With over 90 genes and 110 loci causally implicat... more Deafness is the most frequent sensory disorder. With over 90 genes and 110 loci causally implicated in non-syndromic hearing loss, it is phenotypically and genetically heterogeneous. Here, we investigate the genetic etiology of deafness in four families of Iranian origin segregating autosomal recessive non-syndromic hearing loss (ARNSHL). We used a combination of linkage analysis, homozygosity mapping, and a targeted genomic enrichment platform to simultaneously screen 90 known deafness-causing genes for pathogenic variants. Variant segregation was confirmed by Sanger sequencing. Linkage analysis and homozygosity mapping showed segregation with the DFNB57 locus on chromosome 10 in two families. Targeted genomic enrichment with massively parallel sequencing identified causal variants in PDZD7: a homozygous missense variant (p.Gly103Arg) in one family and compound heterozygosity for missense (p.Met285Arg) and nonsense (p.Tyr500Ter) variants in the second family. Screening of two addit...
The Iowa orthopaedic journal
A prototype drill guide was developed to improve the accuracy of surgical placement of fibular gr... more A prototype drill guide was developed to improve the accuracy of surgical placement of fibular grafts for the treatment of femoral head necrosis. To document performance, two tantalum beads, one placed on the lateral femoral shaft and the other embedded in the superior portion of the head, were used to define the desired graft tract in a series of seven surrogate femurs. Two orthogonal x-rays of the drill guide mounted on each surrogate femur were taken both before and after drilling. After stylus digitization of each x-ray pair, a computer program calculated the achieved accuracy of the drill. The mean of the absolute error between the desired versus obtained position of the drill tip was 3.68 mm (s.d. 1.24 mm), and the random component of the error was 1.98 mm (s.d. 0.89 mm).
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures
Biophysical Journal, 2015
A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing o... more A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing of protein side chains. Although such interactions between residues are often approximated as being pairwise additive, in reality, higher-order many-body contributions that depend on environment drive hydrophobic collapse and cooperative electrostatics. Beginning from dead-end elimination, we derive the first algorithm, to our knowledge, capable of deterministic global repacking of side chains compatible with many-body energy functions. The approach is applied to seven PCNA x-ray crystallographic data sets with resolutions 2.5-3.8 Å (mean 3.0 Å) using an open-source software. While PDB_REDO models average an Rfree value of 29.5% and MOLPROBITY score of 2.71 Å (77th percentile), dead-end elimination with the polarizable AMOEBA force field lowered Rfree by 2.8-26.7% and improved mean MOLPROBITY score to atomic resolution at 1.25 Å (100th percentile). For structural biology applications that depend on side-chain repacking, including x-ray refinement, homology modeling, and protein design, the accuracy limitations of pairwise additivity can now be eliminated via polarizable or quantum mechanical potentials.
High-Throughput Genetic Testing for Thrombotic Microangiopathies and C3 Glomerulopathies
Journal of the American Society of Nephrology : JASN, Jan 17, 2015
The thrombotic microangiopathies (TMAs) and C3 glomerulopathies (C3Gs) include a spectrum of rare... more The thrombotic microangiopathies (TMAs) and C3 glomerulopathies (C3Gs) include a spectrum of rare diseases such as atypical hemolytic uremic syndrome, thrombotic thrombocytopenic purpura, C3GN, and dense deposit disease, which share phenotypic similarities and underlying genetic commonalities. Variants in several genes contribute to the pathogenesis of these diseases, and identification of these variants may inform the diagnosis and treatment of affected patients. We have developed and validated a comprehensive genetic panel that screens all exons of all genes implicated in TMA and C3G. The closely integrated pipeline implemented includes targeted genomic enrichment, massively parallel sequencing, bioinformatic analysis, and a multidisciplinary conference to analyze identified variants in the context of each patient's specific phenotype. Herein, we present our 1-year experience with this panel, during which time we studied 193 patients. We identified 17 novel and 74 rare variant...
Polarizable Force Fields for Biomolecular Modeling
Reviews in Computational Chemistry, 2015
ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. T... more ABSTRACT This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction to the basic principles and formulae underlying alternative models. It reviews recent progress of several well-developed polarizable force fields. Finally, the chapter presents applications of polarizable models to a range of molecular systems, including water and other small molecules, ion solvation, peptides, proteins, and lipid systems. Beyond polarization, modeling the conformational flexibility and corresponding intermolecular energetics of organic molecules via sampling methods such as molecular dynamics is essential to predicting the thermodynamic properties of crystals. The importance of polarization still needs to be established systematically for a wide range of biological systems.
J. Chem. Theory Comput., 2014
The solubility of organic molecules is of critical importance to the pharmaceutical industry; how... more The solubility of organic molecules is of critical importance to the pharmaceutical industry; however, robust computational methods to predict this quantity from firstprinciples are lacking. Solubility can be computed from a thermodynamic cycle that decomposes standard state solubility into the sum of solid−vapor sublimation and vapor−liquid solvation free energies ΔG solubility°= ΔG sub°+ ΔG solv°. Over the past few decades, alchemical simulation methods to compute solvation free energy using classical force fields have become widely used. However, analogous methods for determining the free energy of the sublimation/deposition phase transition are currently limited by the necessity of a priori knowledge of the atomic coordinates of the crystal. Here, we describe progress toward an alternative scheme based on growth of the asymmetric unit into a crystal via alchemy (GAUCHE). GAUCHE computes deposition free energy ΔG dep°= −ΔG sub°= −k B T ln(V c /V g ) + ΔG AU + ΔG AU→UC as the sum of an entropic term to account for compressing a vapor at 1 M standard state (V g ) into the molar volume of the crystal (V c ), where k B is Boltzmann's constant and T is temperature in degrees Kelvin, plus two simulation steps. In the first simulation step, the deposition free energy ΔG AU for a system composed of only N AU asymmetric unit (AU) molecule(s) is computed beginning from an arbitrary conformation in vacuum. In the second simulation step, the change in free energy ΔG AU→UC to expand the asymmetric unit degrees of freedom into a unit cell (UC) composed of N UC independent molecules is computed. This latter step accounts for the favorable free energy of removing the constraint that every symmetry mate of the asymmetric unit has an identical conformation and intermolecular interactions. The current work is based on NVT simulations, which requires knowledge of the crystal space group and unit cell parameters from experiment, but not a priori knowledge of crystalline atomic coordinates. GAUCHE was applied to 5 organic molecules whose sublimation free energy has been measured experimentally, based on the polarizable AMOEBA force field and more than a microsecond of sampling per compound in the program Force Field X. The mean unsigned and RMS errors were only 1.6 and 1.7 kcal/mol, respectively, which indicates that GAUCHE is capable of accurate prediction of absolute sublimation thermodynamics.
2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2009
The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a... more The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability.
Quarterly reviews of biophysics, 2012
An understanding of molecular interactions is essential for insight into biological systems at th... more An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of t...
The Journal of Physical Chemistry B, 2010
Molecular force fields have been approaching a generational transition over the past several year... more Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
Structure, 2011
Most current crystallographic structure refinements augment the diffraction data with a priori in... more Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.
Proteins: Structure, Function, and Bioinformatics, 2009
Here, we summarize the assessment of protein structure refinement in CASP8. Twenty-four groups re... more Here, we summarize the assessment of protein structure refinement in CASP8. Twenty-four groups refined a total of twelve target proteins. Averaging over all groups and all proteins, there was no net improvement over the original starting models. However, there are now some individual research groups who consistently do improve protein structures relative to a starting starting model. We compare various measures of quality assessment, including (i) standard backbone-based methods, (ii) new methods from the Richardson group, and (iii) ensemble-based methods for comparing experimental structures, such as NMR NOE violations and the suitability of the predicted models to serve as templates for molecular replacement. On the whole, there is a general correlation among various measures. However, there are interesting differences. Sometimes a structure that is in better agreement with the experimental data is judged to be slightly worse by GDT-TS. This suggests that for comparing protein structures that are already quite close to the native, it may be preferable to use ensemble-based experimentally derived measures of quality, in addition to single-structure-based methods such as GDT-TS.
A SURGICAL GUIDE TO ACCURATELY PLACE PINS OR NAILS WITHIN THE FEMORAL HEAD
Journal of Musculoskeletal Research, 1999
Journal of Computational Chemistry, 2009
We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsi... more We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The binding free energies calculated from explicit solvent simulations are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. We analyzed the molecular dipole moments of the ligands in gas, water and protein environments. Neither binding affinity nor ligand solvation free energy in bulk water shows much dependence on the molecular dipole moments of the ligands. Substitution of the aromatic or the charged group in the ligand results in considerable change in the solvation energy in bulk water and protein whereas the binding affinity varies insignificantly due to cancellation. The effect of chemical modification on ligand charge distribution is mostly local. Replacing benzene with diazine has minimal impact on the atomic multipoles at the amidinium group. We have also utilized an implicit solvent based end-state approach to evaluate the binding free energies of these inhibitors. In this approach, the polarizable multipole model combined with Poisson-Boltzmann/surface area (PMPB/ SA) provides the electrostatic interaction energy and the polar solvation free energy. Overall the relative binding free energies obtained from the MM-PMPB/SA model are in good agreement with the experimental data. q
Journal of Chemical Theory and Computation, 2007
The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the P... more The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the Poisson equation useful for predicting the electrostatic component of the solvation free energy for solutes ranging in size from small organic molecules to large macromolecular complexes. This work presents a new continuum electrostatics model based on Kirkwood's analytic result for the electrostatic component of the solvation free energy for a solute with arbitrary charge distribution. Unlike GB, which is limited to monopoles, our generalized Kirkwood (GK) model can treat solute electrostatics represented by any combination of permanent and induced atomic multipole moments of arbitrary degree. Here we apply the GK model to the newly developed Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, which includes permanent atomic multipoles through the quadrupole and treats polarization via induced dipoles. A derivation of the GK gradient is presented, which enables energy minimization or molecular dynamics of an AMOEBA solute within a GK continuum. For a series of 55 proteins, GK electrostatic solvation free energies are compared to the Polarizable Multipole Poisson-Boltzmann (PMPB) model and yield a mean unsigned relative difference of 0.9%. Additionally, the reaction field of GK compares well to that of the PMPB model, as shown by a mean unsigned relative difference of 2.7% in predicting the total solvated dipole moment for each protein in this test set. The CPU time needed for GK relative to vacuum AMOEBA calculations is approximately a factor of 3, making it suitable for applications that require significant sampling of configuration space.
The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field
Journal of Chemical Theory and Computation, 2012
An important unsolved problem in materials science is prediction of the thermodynamic stability o... more An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
Journal of Chemical Theory and Computation, 2014
ABSTRACT n this paper we investigate various numerical strategies to compute the direct space pol... more ABSTRACT n this paper we investigate various numerical strategies to compute the direct space polarization energy and associated forces in the context of the point dipole approximation (including damping) used in polarizable molecular dynamics. We present a careful mathematical analysis of the algorithms that have been implemented in popular production packages and applied to large test systems. We show that the classical Jacobi Over-Relaxation method (JOR) should not be used as its convergence requires a proper value of the relaxation parameter, whereas other strategies should be preferred. On a single node, Preconditioned Conjugate Gradient methods (PCG) and Jacobi algorithm coupled with the Direct Inversion in the Iterative Subspace (JI/DIIS) provide reliable stability /convergence and are roughly twice as fast as JOR. Moreover both algorithms are suitable for massively parallel implementations. The lower requirements in terms of processes communications make JI/DIIS the method of choice for MPI and hybrid OpenMP/MPI paradigms for real life tests. Furthermore, using a predictor step as a guess along a molecular dynamics simulation provides another inexpensive, yet very effective form of convergence acceleration. Overall, two to three orders of magnitude in time can be gained compared to the initial JOR single node approach to the final PGC or JI/DIIS parallel one combined with the predictors MD refinements. Such a speedup traces a new route for the high performance implementation of polarizable molecular dynamics and therefore extends the applicability of the technique as it will facilitate future multiscale QM/MM/continuum computations.
The Journal of Chemical Physics, 2007
Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solve... more Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager used vacuum properties of small molecules, including polarizability, dipole moment and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we describe the theory underlying a newly developed Polarizable Multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK a prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2-13 kcal/mole, depending on the formal charge of the protein, but had only a small influence on dipole moments.
Computational Insights for the Discovery of Non-ATP Competitive Inhibitors of MAP Kinases
Current Drug Metabolism, 2012
Due to their role in cellular signaling mitogen activated protein (MAP) kinases represent targets... more Due to their role in cellular signaling mitogen activated protein (MAP) kinases represent targets of pharmaceutical interest. However, the majority of known MAP kinase inhibitors compete with cellular ATP and target an ATP binding pocket that is highly conserved in the 500 plus representatives of the human protein kinase family. Here we review progress toward the development of non-ATP competitive MAP kinase inhibitors for the extracellular signal regulated kinases (ERK1/2), the c-jun N-terminal kinases (JNK1/2/3) and the p38 MAPKs (α, β, γ, and δ). Special emphasis is placed on the role of computational methods in the drug discovery process for MAP kinases. Topics include recent advances in X-ray crystallography theory that improve the MAP kinase structures essential to structurebased drug discovery, the use of molecular dynamics to understand the conformational heterogeneity of the activation loop and inhibitors discovered by virtual screening. The impact of an advanced polarizable force field such as AMOEBA used in conjunction with sophisticated kinetic and thermodynamic simulation methods is also discussed.
Bayesian Modeling of Crystallographic Disorder
Biophysical Journal, 2012
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Papers by Michael Schnieders