Note: On the universality of proximal radial distribution functions of proteins.
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ABSTRACT:
SUBMITTER: Lin B
PROVIDER: S-EPMC3069986 | biostudies-literature | 2011 Mar
REPOSITORIES: biostudies-literature
Publications
Note: On the universality of proximal radial distribution functions of proteins.
Lin Bin B Pettitt B Montgomery BM
The Journal of chemical physics 20110301 10
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Project description:The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.
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Project description:The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.
| S-EPMC8439718 | biostudies-literature
Project description:Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute-solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute-solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute-solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ∼ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems.
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Project description:We consider the hydration structure and thermodynamic energetics of solutes in aqueous solution. On the basis of the dominant local correlation between the solvent and the chemical nature of the solute atoms, proximal distribution functions (pDF) can be used to quantitatively estimate the hydration pattern of the macromolecules. We extended this technique to study the solute-solvent energetics including the van der Waals terms representing excluded volume and tested the method with butane and propanol. Our results indicate that the pDF-reconstruction algorithm can reproduce van der Waals solute-solvent interaction energies to useful kilocalorie per mole accuracy. We subsequently computed polyalanine-water interaction energies for a variety of conformers, which also showed agreement with the simulated values.
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Project description:We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
| S-EPMC6790663 | biostudies-literature
Project description:The structural properties of three- and four-site water models are improved by extending the ForceBalance parametrization code to include a new methodology allowing for the targeting of any radial distribution function (RDF) during the parametrization of a force field. The mean squared difference (MSD) between the experimental and simulated RDFs contributes to an objective function, allowing for the systematic optimization of force field parameters to reach closer overall agreement with experiment. RDF fitting is applied to develop modified versions of the TIP3P and TIP4P/2005 water models in which the Lennard-Jones potential is replaced by a Buckingham potential. The optimized TIP3P-Buckingham and TIP4P-Buckingham potentials feature 93 and 98% lower MSDs in the OO RDF compared to the TIP3P and TIP4P/2005 models respectively, with marked decreases in the height of the first peak. Additionally, these Buckingham models predict the entropy of water more accurately, reducing the error in the entropy of TIP3P from 11 to 3% and the error in the entropy of TIP4P/2005 from 11 to 2%. These new Buckingham models have improved predictive power for many nonfitted properties particularly in the case of TIP3P. Our work directly demonstrates how the Buckingham potential can improve the description of water's structural properties beyond the Lennard-Jones potential. Moreover, adding a Buckingham potential is a favorable alternative to adding interaction sites in terms of computational speed on modern GPU hardware.
| S-EPMC6175054 | biostudies-literature
Project description:Techniques to calculate the free energy changes of a system are very useful in the study of biophysical and biochemical properties. In practice, free energy changes can be described with thermodynamic cycles, and the free energy change of an individual process can be computed by sufficiently sampling the corresponding configurations. However, this is still time-consuming especially for large biomolecular systems. Previously, we have shown that by utilizing precomputed solute-solvent correlations, so-called proximal distribution functions (pDF), we are capable of reconstructing the solvent environment near solute atoms, thus estimating the solute-solvent interactions and solvation free energies of molecules. In this contribution, we apply the technique of pDF-reconstructions to calculate chemical potentials and use this information in thermodynamic cycles. This illustrates how free energy changes of nontrivial chemical processes in aqueous solution systems can be rapidly estimated.
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Project description:Background and purposeThe objective of this study was to determine diagnostic and prognostic values of proximal radial motor conduction in acute compressive radial neuropathy.MethodsThirty-nine consecutive cases of acute compressive radial neuropathy with radial conduction studies-including stimulation at Erb's point-performed within 14 days from clinical onset were reviewed. The radial conduction data of 39 control subjects were used as reference data.ResultsThirty-one men and eight women (age, 45.2±12.7 years, mean±SD) were enrolled. All 33 patients in whom clinical follow-up data were available experienced complete recovery, with a recovery time of 46.8±34.3 days. Partial conduction block was found frequently (17 patients) on radial conduction studies. The decrease in the compound muscle action potential area between the arm and Erb's point was an independent predictor for recovery time.ConclusionsProximal radial motor conduction appears to be a useful method for the early detection and prediction of prognosis of acute compressive radial neuropathy.
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Project description:Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the alpha-, alpha-beta-, and beta- proteins have the scaling exponents of approximately 1.7, 2.5, and 3.2, respectively. The three classes merge into one when the contact range is truncated at a reasonable value. We elucidate the role of the potential associated with the chirality of a protein.
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Project description:Recent studies have indicated that distal radial access (DRA) is feasible in patients undergoing percutaneous coronary intervention (PCI). The present study aimed to compare DRA, proximal radial access (PRA), and femoral access (FA) in patients with ST-elevation myocardial infarction (STEMI) undergoing PCI. Data were analyzed for 109 patients with STEMI treated via primary PCI from March 2020 to May 2021. The success rate of DRA was 83.3% (35/42), including seven cases of failed puncture (puncture failure = 5, severe radial artery spasm = 2). Primary PCI via the DRA was successful in all 35 patients. After classifying the patients requiring crossover into a separate group, the percentage of the puncture time in the door-to-wiring time was 2.7% [2.2-4.3], 3.3% [2.3-4.0], 2.6% [1.2-4.9], and 27.0% [13.5-29.3] in the DRA (n = 35), PRA (n = 24), FA (n = 26), and crossover (n = 9) groups, respectively (p < 0.01). Only two local hematomas (≤5 cm) occurred in the DRA group, while one patient in the FA group required surgical treatment and a transfusion for an access-site vascular injury. When performed by an experienced operator, DRA may represent a feasible alternative to other access routes in select patients with STEMI undergoing PCI, such as those with a high risk of bleeding.
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