Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands

The energy contributions of various physical interactions to the total Gibbs energy of complex formation of the biologically important DNA hairpin d(GCGAAGC) with aromatic antitumor antibiotics daunomycin and novantron and the mutagens ethidium and proflavine have been calculated. It has been shown that the relatively small value of the total energy of binding of the ligands to the hairpin is the sum of components great in absolute value and different in sign. The contributions of van der Waals interactions and both intra- and intermolecular hydrogen bonds and bonds with aqueous environment have been studied. According to the calculations, the hydrophobic and van der Waals components are energetically favorable in complex formation of the ligands with the DNA pairpin d(GCGAAGC), whereas the electrostatic (with consideration of hydrogen bonds) and entropic components are unfavorable.     

Energetics of complex formation of the dna hairpin structure d(GCGAAGC) with aromatic ligands

The energy contributions of various physical interactions to the total Gibbs energy of complex formation of the biologically important DNA hairpin d(GCGAAGC) with aromatic antitumor antibiotics daunomycin and novantrone and mutagens ethidium bromide and proflavin have been calculated. It has been shown that the relatively small value of the total energy of binding of the ligands to the hairpin is the sum of components great in absolute value and different in sign. The contributions of van der Waals interactions and both intra- and intermolecular hydrogen bonds and bonds with aqueous environment have been studied. According to the calculations, the hydrophobic and van der Waals components are energetically favorable in complex formation of the ligands with the hairpin d(GCGAAGC), whereas the electrostatic (with consideration of hydrogen bonds) and entropic components are unfavorable.     

Probing the electronic structures and properties of neutral and anionic ScSi n (0,−1) (n = 1–6) clusters using ccCA-TM and G4 theory

We apply molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation to investigate and reveal the binding mechanism between five xanthine inhibitors and DPP-4. The electrostatic and van der Waals interactions of the five inhibitors with DPP-4 are analyzed and discussed. The computed binding free energies using MM-PBSA method are in qualitatively agreement with experimental inhibitory potency of five inhibitors. The hydrogen bonds of inhibitors with Ser630 and Asp663 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the key contacts with His740, Asn710, Trp629, and Tyr666 have larger contributions to the binding free energy and play important roles in distinguishing the variant bioactivity of five inhibitors.     

Energetics of protein folding

The energetics of protein folding determine the 3D structure of a folded protein. Knowledge of the energetics is needed to predict the 3D structure from the amino acid sequence or to modify the structure by protein engineering. Recent developments are discussed: major factors are reviewed and auxiliary factors are discussed briefly. Major factors include the hydrophobic factor (burial of non-polar surface area) and van der Waals interactions together with peptide hydrogen bonds and peptide solvation. The long-standing model for the hydrophobic factor (free energy change proportional to buried non-polar surface area) is contrasted with the packing-desolvation model and the approximate nature of the proportionality between free energy and apolar surface area is discussed. Recent energetic studies of forming peptide hydrogen bonds (gas phase) are reviewed together with studies of peptide solvation in solution. Closer agreement is achieved between the 1995 values for protein unfolding enthalpies in vacuum given by Lazaridis-Archontis-Karplus and Makhatadze-Privalov when the solvation enthalpy of the peptide group is taken from electrostatic calculations. Auxiliary factors in folding energetics include salt bridges and side-chain hydrogen bonds, disulfide bridges, and propensities to form alpha-helices and beta-structure. Backbone conformational entropy is a major energetic factor which is discussed only briefly for lack of knowledge.     

Molecular Modeling-Based Energy Analysis of Dimeric Binding of Ligands to the Minor DNA Groove

Molecular-modeling methods have been used to perform energy analysis of dimeric complex formation between lexitropsins and double-stranded DNA. Stabilization of dimeric complexes by hydrophobic and van der Waals interactions has been demonstrated. Electrostatic interactions and the contributions of hydrogen bonds and changes in the number of degrees of freedom had a destabilizing influence. The energy of monomeric and dimeric binding has been compared.     

Contribution of enthalpy to the energetics of complex formation of aromatic ligands with DNA

The energy contributions of electrostatic, van der Waals interactions, hydrogen bonds, and interactions of charge transfer type to the enthalpy of complex formation of the double-stand DNA with the antitumor antibiotics daunomycin, nogalamycin, and novantron, as well as the mutagens ethidium bromide and proflavine have been calculated. According to the calculations, the van der Waals component (except for nogalamycin) is energetically favorable during complex formation of the antibiotics with DNA, and the contributions of H bonds and electrostatic interactions are unfavorable, with the probability of charge transfer in the complexes being low. It has been shown that the relatively low value of the experimental enthalpy of binding is the sum of components greater in absolute value and different in the sign, which is the cause of large errors in estimating the total enthalpy of complex formation of aromatic ligands with DNA.     

Protein docking using continuum electrostatics and geometric fit

The computer program DOT quickly finds low-energy docked structures for two proteins by performing a systematic search over six degrees of freedom. A novel feature of DOT is its energy function, which is the sum of both a Poisson-Boltzmann electrostatic energy and a van der Waals energy, each represented as a grid-based correlation function. DOT evaluates the energy of interaction for many orientations of the moving molecule and maintains separate lists scored by either the electrostatic energy, the van der Waals energy or the composite sum of both. The free energy is obtained by summing the Boltzmann factor over all rotations at each grid point. Three important findings are presented. First, for a wide variety of protein-protein interactions, the composite-energy function is shown to produce larger clusters of correct answers than found by scoring with either van der Waals energy (geometric fit) or electrostatic energy alone. Second, free-energy clusters are demonstrated to be indicators of binding sites. Third, the contributions of electrostatic and attractive van der Waals energies to the total energy term appropriately reflect the nature of the various types of protein-protein interactions studied.     

Torsional relaxation for biopolymers.

We describe a method for making natural, physical movements in a chained polymer by sequentially adjusting a few neighboring torsion angles in the polymer backbone. In addition to being very fast and easy to implement, the method is also very general. It applies equally well to proteins and nucleic acids. This method is then used to design a local refinement procedure. We test the refinement procedure on the minimization of a simple energy function for proteins. The energy function has a simplified potential for hydrophobic interaction, a hydrogen-bond term, and a term for van der Waals interaction. There is considerable current interest in such simple energy functions for protein folding. When applied to refine structures found by a global search method, the refinement is able to produce large reduction in the hydrogen-bond term and the van der Waal term of the energy. We conclude that the method is particularly effective in finding good "packing" of residues in an initially compact conformation.     

Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49

To address how proteins recognize polyether toxin compounds, we focused on the interaction between the ABC ring compound of ciguatoxin 3C and its specific antibody, 1C49. Surface plasmon resonance analyses indicated that Escherichia coli-expressed variable domain fragments (Fv) of 1C49 had the high affinity constants and slow dissociation constants typical of antigen-antibody interactions. Linear van't Hoff analyses suggested that the interaction is enthalpy-driven. We resolved the crystal structure of 1C49 Fv bound to ABC ring compound of ciguatoxin 3C at a resolution of 1.7A. The binding pocket of the antibody had many aromatic rings and bound the antigen by shape complementarity typical of hapten-antibody interactions. Three hydrogen bonds and many van der Waals interactions were present. We mutated several residues of the antibody to Ala, and we used surface plasmon resonance to analyze the interactions between the mutated antibodies and the antigen. This analysis identified Tyr-91 and Trp-96 in the light chain as hot spots for the interaction, and other residues made incremental contributions by conferring enthalpic advantages and reducing the dissociation rate constant. Systematic mutation of Tyr-91 indicated that CH-pi and pi-pi interactions between the aromatic ring at this site and the antigen made substantial contributions to the association, and van der Waals interactions inhibited dissociation, suggesting that aromaticity and bulkiness are critical for the specific recognition of polyether compounds by proteins.     

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions

The non-polar component of the potential of mean force of dimerization of alanine dipeptide has been calculated in explicit solvent by free energy perturbation. We observe that the calculated PMF is inconsistent with a non-polar hydration free energy model based solely on the solute surface area. The non-linear behavior of the solute-solvent van der Waals energy is primarily responsible for the non-linear dependence of the potential of mean force with respect to the surface area. The calculated potential of mean force is reproduced by an implicit solvent model based on a solvent continuum model for the solute-solvent van der Waals interaction energy and the surface area for the work of forming the solute cavity.     

A free energy analysis of nucleic acid base stacking in aqueous solution.

This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are treated by using the finite difference Poisson-Boltzmann method and nonpolar effects are treated with explicit calculation of van der Waals interactions and/or free energy-surface area relationships. Although for some pairs of bases there is a favorable Coulombic interaction in the stacked conformation, generally the net effect of electrostatic interactions is to oppose stacking. This result is caused by the loss of favorable base-solvent electrostatic interactions, that accompany the partial removal of polar atoms from water in the stacked conformation. Nonpolar interactions, involving the hydrophobic effect and enhancement of van der Waals interactions caused by close-packing, drive stacking. The calculations qualitatively reproduce the experimental dependence of stacking free energy on purine-pyrimidine composition.     

Life at the border: Adaptation of proteins to anisotropic membrane environment

This review discusses main features of transmembrane (TM) proteins which distinguish them from water‐soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co‐translational and post‐translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large‐scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen‐bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region—between double bonds and carbonyl groups of lipids. These “midpolar” regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side‐chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein–lipid binding.     

De novo protein design. I. In search of stability and specificity.

We have developed a fully automated protein design strategy that works on the entire sequence of the protein and uses a full atom representation. At each step of the procedure, an all-atom model of the protein is built using the template protein structure and the current designed sequence. The energy of the model is used to drive a Monte Carlo optimization in sequence space: random moves are either accepted or rejected based on the Metropolis criterion. We rely on the physical forces that stabilize native protein structures to choose the optimum sequence. Our energy function includes van der Waals interactions, electrostatics and an environment free energy. Successful protein design should be specific and generate a sequence compatible with the template fold and incompatible with competing folds. We impose specificity by maintaining the amino acid composition constant, based on the random energy model. The specificity of the optimized sequence is tested by fold recognition techniques. Successful sequence designs for the B1 domain of protein G, for the lambda repressor and for sperm whale myoglobin are presented. We show that each additional term of the energy function improves the performance of our design procedure: the van der Waals term ensures correct packing, the electrostatics term increases the specificity for the correct native fold, and the environment solvation term ensures a correct pattern of buried hydrophobic and exposed hydrophilic residues. For the globin family, we show that we can design a protein sequence that is stable in the myoglobin fold, yet incompatible with the very similar hemoglobin fold.     

Solvent accessibilities in glycyl, alanyl and seryl dipeptides.

Theoretical studies on glycyl-alanyl and seryl dipeptides were performed to determine the probable backbone and side-group conformations that are preferred for solvent interaction. By following the method of Lee & Richards [(1971) J. Mol. Biol. 55, 379-400], a solute molecule is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, and a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the surface accessible to the solvent molecule, and hence the solvent accessibility for a particular conformation of the solute molecule, is computed. From the calculated solvent accessibilities for various conformations, solvation maps for dipeptides were constructed. These solvation maps suggest that the backbone polar atoms could interact with solvent molecules selectively, depending on the backbone conformation. A conformation in the right-handed bridge (zetaR) region is favoured for both solvent interaction and intrachain hydrogen-bonding. Also the backbone side-chain hydrogen-bonding within the same dipeptide fragment in proteins is less favoured than hydrogen-bonding between side chain and water and between side chain and atoms of other residues. Solvent accessibilities suggest that very short distorted alphaR-helical and extended-structural parts may be stabilized via solvent interaction, and this could easily be possible at the surface of the protein molecules, in agreement with protein-crystal data.     

Energetic analysis of binding of progesterone and 5 beta-androstane-3,17-dione to anti-progesterone antibody DB3 using molecular dynamics and free energy calculations.

Molecular dynamics simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) free energy calculations were used to study the energetics of the binding of progesterone (PRG) and 5 beta-androstane-3,17-dione (5AD) to anti-PRG antibody DB3. Although the two steroids bind to DB3 in different orientations, their binding affinities are of the same magnitude, 1 nM for PRG and 8 nM for 5AD. The calculated relative binding free energy of the steroids, 8.8 kJ/mol, is in fair agreement with the experimental energy, 5.4 kJ/mol. In addition, computational alanine scanning was applied to study the role of selected amino acid residues of the ligand-binding site on the steroid cross-reactivity. The electrostatic and van der Waals components of the total binding free energies were found to favour more the binding of PRG, whereas solvation energies were more favourable for the binding of 5AD. The differences in the free energy components are due to the binding of the A rings of the steroids to different binding pockets: PRG is bound to a pocket in which electrostatic antibody-steroid interactions are dominating, whereas 5AD is bound to a pocket in which van der Waals and hydrophobic interactions dominate.     

Thermodynamics of barnase unfolding.

The thermodynamics of barnase denaturation has been studied calorimetrically over a broad range of temperature and pH. It is shown that in acidic solutions the heat denaturation of barnase is well approximated by a 2-state transition. The heat denaturation of barnase proceeds with a significant increase of heat capacity, which determines the temperature dependencies of the enthalpy and entropy of its denaturation. The partial specific heat capacity of denatured barnase is very close to that expected for the completely unfolded protein. The specific denaturation enthalpy value extrapolated to 130 degrees C is also close to the value expected for the full unfolding. Therefore, the calorimetrically determined thermodynamic characteristics of barnase denaturation can be considered as characteristics of its complete unfolding and can be correlated with structural features--the number of hydrogen bonds, extent of van der Waals contacts, and the surface areas of polar and nonpolar groups. Using this information and thermodynamic information on transfer of protein groups into water, the contribution of various factors to the stabilization of the native structure of barnase has been estimated. The main contributors to the stabilization of the native state of barnase appear to be intramolecular hydrogen bonds. The contributions of van der Waals interactions between nonpolar groups and those of hydration effects of these groups are not as large if considered separately, but the combination of these 2 factors, known as hydrophobic interactions, is of the same order of magnitude as the contribution of hydrogen bonding.     

Role of Hydrogen Bonds in Protein-DNA Recognition: A Comparison of Generalized Born and Finite Difference Poisson-Boltzmann Solvation Treatments

Abstract

Hydrogen bonds have been accredited with a major role historically, in the formation and stabilization of biomolecular structures. The formation of hydrogen bonds at protein-DNA interfaces in aqueous medium involves not only favorable interactions of the donor and acceptor functional groups but also a loss of interactions between these groups with the solvent water. We have investigated the energetics of about 500 potential hydrogen bonds occuring at protein-DNA interfaces incorporating some recent improvements in biomolecular force fields and solvation treatments. We present here results of our assessment of hydrogen bond contributions to the overall standard free energy of formation of protein-DNA complexes obtained with the generalized Born model and finite difference Poisson- Boltzmann methodology for solvation in conjunction with AMBER force field. Our results support the emerging view on the role of electrostatics in general and that of hydrogen bonds in particular which is that hydrogen bonds do not drive protein-DNA complex formation by virtue of the unfavourable cost of the electrostatics of desolvation. They however, act to stabilize the complex once it is formed.     

Solvent effects and polar interactions in the structural stability and dynamics of globular proteins.

Using detailed hydrogen bonding, surface exposure, internal environment, and solvent interaction calculations on several proteins, in conjunction wit data from quantum mechanical hydrogen-bonding studies, various contributions to the free energy of globular estimated and their likely relative significance discussed. A picture emerges of globular proteins as extremely well-fitting jigsaw-puzzles, in which no single driving force dominates the marginal stability of the native conformation. Rather, the folded structure is seen as the result of a complex global maximization of several strongly-interacting driving forces. In particular, the necessity to maintain very efficient internal hydrogen-bonding, and the role of the solvent as a hydrogen-bond sink, are stressed as strong constraints on the (incomplete) maximization of hydrophobic effects. The possible significance of internal dipole-induced dipole interactions is discussed tentatively. Although quantitative estimates of the various contributions remain uncertain, consideration of effective force constants suggests that polar, including solvent, interactions may largely determine the overall curvatures of the native conformation's potential well, and be important in controlling the flexibility of local regions which are important for the exact positioning of groups during enzyme catalysis, as well as the molecule's overall dynamics. In contrast, hydrophobic interactions change less for small geometrical perturbations, and seem more relevant to directing the folding protein. along a path to a region in configurational space where the polar interactions can switch on for the final "docking".     

Atomic-scale analysis of the solvation thermodynamics of hydrophobic hydration.

Molecular dynamics simulations are used to model the transfer thermodynamics of krypton from the gas phase into water. Extra long, nanosecond simulations are required to reduce the statistical uncertainty of the calculated "solvation" enthalpy to an acceptable level. Thermodynamic integration is used to calculate the "solvation" free energy, which together with the enthalpy is used to calculate the "solvation" entropy. A comparison series of simulations are conducted using a single Lennard-Jones sphere model of water to identify the contribution of hydrogen bonding to the thermodynamic quantities. In contrast to the classical "iceberg" model of hydrophobic hydration, the favorable enthalpy change for the transfer process at room temperature is found to be due primarily to the strong van der Waals interaction between the solute and solvent. Although some stabilization of hydrogen bonding does occur in the solvation shell, this is overshadowed by a destabilization due to packing constraints. Similarly, whereas some of the unfavorable change in entropy is attributed to the reduced rotational motion of the solvation shell waters, the major component is due to a decrease in the number of positional arrangements associated with the translational motions.