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The electric polarizability of DNA, represented by the dielectric constant, is a key intrinsic property that modulates DNA interaction with effector proteins. Surprisingly, it has so far remained unknown owing to the lack of experimental tools able to access it. Here, we experimentally resolved it by detecting the ultraweak polarization forces of DNA inside single T7 bacteriophages particles using electrostatic force microscopy. In contrast to the common assumption of low-polarizable behavior like proteins (εr ∼ 2-4), we found that the DNA dielectric constant is ∼ 8, considerably higher than the value of ∼ 3 found for capsid proteins. State-of-the-art molecular dynamic simulations confirm the experimental findings, which result in sensibly decreased DNA interaction free energy than normally predicted by Poisson-Boltzmann methods. Our findings reveal a property at the basis of DNA structure and functions that is needed for realistic theoretical descriptions, and illustrate the synergetic power of scanning probe microscopy and theoretical computation techniques.

There is increasing evidence for the presence of an alternative code imprinted in the genome that might contribute to gene expression regulation through an indirect reading mechanism. In mammals, components of this coarse-grained regulatory mechanism include chromatin structure and epigenetic signatures, where d(CpG) nucleotide steps are key players. We report a comprehensive experimental and theoretical study of d(CpG) steps that provides a detailed description of their physical characteristics and the impact of cytosine methylation on these properties. We observed that methylation changes the physical properties of d(CpG) steps, having a dramatic effect on enriched CpG segments, such as CpG islands. We demonstrate that methylation reduces the affinity of DNA to assemble into nucleosomes, and can affect nucleosome positioning around transcription start sites. Overall, our results suggest a mechanism by which the basic physical properties of the DNA fiber can explain parts of the cellular epigenetic regulatory mechanisms., (Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

The IEF-MST continuum solvation model is used to predict the hydration free energies and tautomeric preferences of a set of multifunctional compounds compiled as a blind test for computational solvation methods in the SAMPL2 contest. Computations of hydration free energies was performed using both HF/6-31G(d) and B3LYP/6-31G(d) versions of the IEF-MST model. For tautomeric preferences, the IEF-MST data was combined with the gas phase free energy differences predicted at different levels of theory ranging from MP2/6-31+G(d) to MP2/CBS+[CCSD-MP2/6-31+G(d)] levels. Comparison with the experimental data provided for hydration free energies yields a root-mean square deviation (rmsd) close to 2.3 kcal/mol, which is quite remarkable, especially considering the reduced set of training compounds used in the parametrization of the IEF-MST method. With regard to tautomerism, the lowest error in the prediction of the relative stabilities between tautomers in solution is obtained by combining MP2/CBS+[CCSD-MP2/6-31+G(d)] results with IEF-MST hydration free energies, yielding a rmsd of ca. 3.4 kcal/mol. The results illustrate the delicate balance that must be kept between the intrinsic relative stabilities in the gas phase and the differential hydration preferences in order to obtain an accurate description of the prototropic tautomerism in bioorganic compounds.

We present here a molecular dynamics study on a promising class of peptide nanotubes with a partially hydrophobic inner cavity and an easy chemical functionalization of the lumen of the cylindrical structure. The structural and dynamical behavior of the nanotube in water, methanol, and chloroform has been analyzed using state of the art theoretical methods. The nanotube structure is always well preserved, but solvent-dependent dynamic alterations are evident. Such dynamic effects are surprisingly more severe in the most viscous solvent (water), as a consequence of the competition in polar solvents between intra- and intermolecular hydrogen bonds. Stiffness analysis from the collected trajectories helped us to characterize the equilibrium deformability of the nanotube, while steered dynamics simulations were used to determine the magnitude of free energy associated with nanotube growth. Analysis of the carrier and permeation properties of the compounds reveals surprising properties: (i) permeability for the most polar solvent (water), (ii) carrier properties for the most apolar solvent (chloroform), and (iii) neither good permeation nor carrier properties for the intermediate solvent in polarity (methanol). Results reported here constitute the most extensive characterization of these nanotubes presented to date and open many intriguing questions on their stability, dynamics, and transport/carrier properties.

The IEF-MST continuum solvation model is used to predict the hydration free energies of a set of 63 multifunctional compounds very recently compiled as a blind test (denoted SAMPL1) for computational solvation methods (Guthrie, J. P. J. Phys. Chem. B 2009, 113, 4501). Computations were performed using the IEF-MST versions parametrized at both HF/6-31G(d) and B3LYP/6-31G(d) levels. For direct comparison with other methods, computations were performed using the frozen geometries provided with the SAMPL1 data set, as well as the gas phase optimized geometries following the implementation of the IEF-MST model. Comparison with experimental data yields a root-mean square deviation for the whole set of compounds of 2.7 and 2.4 kcal/mol at both HF and B3LYP levels. The agreement between IEF-MST and experimental data is then quite remarkable, especially considering the reduced set of training compounds (72 data in water) used in the parametrization of the IEF-MST method.

In a recent Account, Cramer and Truhlar presented a comparison between the SM8 method and standard versions of other continuum solvation models implemented in widely available quantum mechanical programs. In that Account, the SM8 model was found to lead to "considerably smaller errors for aqueous and nonaqueous free energies of solvation for neutrals, cations, and anions, with particularly good performance for nonaqueous data". Here, we demonstrate that competing solvation methods are indeed as accurate as the SM8 method, if they are applied with the same rigor.

Summary: DNAlive is a tool for the analysis and graphical display of structural and physical characteristics of genomic DNA. The web server implements a wide repertoire of metrics to derive physical information from DNA sequences with a powerful interface to derive 3D information on large sequences of both naked and protein-bound DNAs. Furthermore, it implements a mesoscopic Metropolis code which allows the inexpensive study of the dynamic properties of chromatin fibers. In addition, our server also surveys other protein and genomic databases allowing the user to combine and explore the physical properties of selected DNA in the context of functional features annotated on those regions., Availability: http://mmb.pcb.ub.es/DNAlive/ ; http://www.inab.org/

The structure and dynamic properties of different antisense related duplexes (DNA x RNA, 2'O-Me-DNA x RNA, 2'F-ANA x RNA, C5(Y)-propynyl-DNA x RNA, ANA x RNA, and control duplexes DNA x DNA and RNA x RNA) have been determined by means of long molecular dynamics simulations (covering more than 0.5 micros of fully solvated unrestrained MD simulation). The massive analysis presented here allows us to determine the subtle differences between the different duplexes, which in all cases pertain to the same structural family. This analysis provides information on the molecular determinants that allow RNase H to recognize and degrade some of these duplexes, whereas others with apparently similar conformations are not affected. Subtle structural and deformability features define the key properties used by RNase H to discriminate between duplexes.

The need to simulate large-sized molecules or to deal with large series of compounds is a challenging topic in computational chemistry, which has stimulated the development of accurate semiempirical methods, such as the recently reported Recife Model 1 (RM1; J Comput Chem 2006, 27, 1101). Even though RM1 may prove to be of value simply due to the enhanced quantitative accuracy in gas phase, it is unclear how the new parameters optimized for RM1 affect the suitability of this semiempirical Hamiltonian to study chemical processes in condensed phases. To address this question, we report the parametrization of the MST/RM1 continuum model for neutral solutes in water, octanol, chloroform and carbon tetrachloride, and for ions in water. The results are used to discuss the transferability of the solvation parameters implemented in previous MST/AM1 and MST/PM3 models.

The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations.

We report a systematic comparison of the dispersion and repulsion contributions to the free energy of solvation determined using quantum mechanical self-consistent reaction field (QM-SCRF) and classical methods. In particular, QM-SCRF computations have been performed using the dispersion and repulsion expressions developed in the framework of the integral equation formalism of the polarizable continuum model, whereas classical methods involve both empirical pairwise potential and surface-dependent approaches. Calculations have been performed for a series of aliphatic and aromatic compounds containing prototypical functional groups in four solvents: water, octanol, chloroform, and carbon tetrachloride. The analysis is focused on the dependence of the dispersion and repulsion components on the level of theory used in QM-SCRF computations, the contribution of those terms in different solvents, and the magnitude of the coupling between electrostatic and dispersion-repulsion components. Finally, comparison is made between the dispersion-repulsion contributions obtained from QM-SCRF calculations and the results determined from classical approaches., (Copyright 2006 Wiley Periodicals, Inc.)

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile.

PMUT allows the fast and accurate prediction (approximately 80% success rate in humans) of the pathological character of single point amino acidic mutations based on the use of neural networks. The program also allows the fast scanning of mutational hot spots, which are obtained by three procedures: (1) alanine scanning, (2) massive mutation and (3) genetically accessible mutations. A graphical interface for Protein Data Bank (PDB) structures, when available, and a database containing hot spot profiles for all non-redundant PDB structures are also accessible from the PMUT server.

We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules., ((c) 2004 Wiley-Liss, Inc.)

The counterion distribution around a DNA dodecamer (5'-CGCGAATTCGCG-3') is analyzed using both standard and novel techniques based on state of the art molecular dynamics simulations. Specifically, we have explored the population of Na(+) in the minor groove of DNA duplex, and whether or not a string of Na(+) can replace the spine of hydration in the narrow AATT minor groove. The results suggest that the insertion of Na(+) in the minor groove is a very rare event, but that when once the ion finds specific sites deep inside the groove it can reside there for very long periods of time. According to our simulation the presence of Na(+) inside the groove does not have a dramatic influence in the structure or dynamics of the duplex DNA. The ability of current MD simulations to obtain equilibrated pictures of the counterion atmosphere around DNA is critically discussed.

Different theoretical methods for the description of nucleic acid structures are reviewed. Firstly, we introduce the concept of classical force-field in the context of nucleic acid structures, discussing their accuracy. We then examine theoretical approaches to the description of nucleic acids based on: i) a rigid or quasi-rigid description of the molecule, ii) molecular mechanics optimization, and iii) molecular dynamics. Special emphasis is made ion current state of the art molecular dynamics simulations of nucleic acids structures.

Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure-activity relationships., (Copyright 2003 Wiley Periodicals, Inc.)

The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. Attention is paid to i) the reliability of semiempirical versus ab initio treatments of the quantum mechanical molecule, ii) the role of solvation, and iii) the effect of including the polarization energy component in the calculation of the GMIPp functional. The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds.