Energetics Of Conformational Changes Research Articles

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems.

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Crystal structures of N-[4-(tri-fluoro-meth-yl)phen-yl]benzamide and N-(4-meth-oxy-phen-yl)benz-amide at 173 K: a study of the energetics of conformational changes due to crystal packing.

As a part of our study of the syntheses of aryl amides, the crystal structures of two benzamides were determined from single-crystal X-ray data at 173 K. Both crystal structures contain mol-ecular units as asymmetric units with no solvent in the unit cells. Crystal structure I, TFMP, is the result of the crystallization of N-[4-(tri-fluoro-meth-yl)phen-yl]benzamide, C14H10F3NO. Crystal structure II, MOP, is composed of N-(4-meth-oxy-phen-yl)benzamide, C14H13NO2, units. TFMP is triclinic, space group P , consisting of two mol-ecules in the unit cell related by the center of symmetry. MOP is monoclinic, space group P21/c, consisting of four mol-ecules in the unit cell. Both types of mol-ecules contain three planar regions; a phenyl ring, an amide planar region, and a para-substituted phenyl ring. The orientations of these planar regions within the asymmetric units are compared to their predicted orientations, in isolation, from DFT calculations. The aryl rings are tilted approximately 60° with respect to each other in both experimentally determined structures, as compared to 30° in the DFT results. These conformational changes result in more favorable environments for N-H⋯O hydrogen bonding and aryl ring π-stacking in the crystal structures. Inter-molecular inter-actions were examined by Hirshfeld surface analysis and qu-anti-fied by calculating mol-ecular inter-action energies. The results of this study demonstrate that both hydrogen bonding and dispersion are essential to the side-by-side stacking of mol-ecular units in these crystal structures. Weaker dispersion inter-actions along the axial directions of the mol-ecules reveal insight into the melting mechanisms of these crystals.

Single-molecule binding dynamics and cooperativity of the first two cyclic nucleotides at the TAX-4 CNG channel

Binding of ligands to multiple active sites in oligomeric proteins is an important phenomenon for many biological processes. The kinetics of distinct binding events directly relate to the energetics of conformational changes underlying both binding and cooperative interactions between sites. However, these dynamics are rarely directly observed and are occluded in ensemble measures due to averaging over mixtures of bound conformations and asynchronous events. Single-molecule (SM) approaches are powerful tools for resolving these asynchronous dynamics, but their application to studies of membrane proteins is challenged by costly sample preparation, degradation of protein function in nonnative lipid environments such as detergents, and lack of solution access to intracellular binding sites.

On the link between conformational changes, ligand binding and heat capacity

BackgroundConformational changes coupled to ligand binding constitute the structural and energetics basis underlying cooperativity, allostery and, in general, protein regulation. These conformational rearrangements are associated with heat capacity changes. ITC is a unique technique for studying binding interactions because of the simultaneous determination of the binding affinity and enthalpy, and for providing the best estimates of binding heat capacity changes. Scope of reviewStill controversial issues in ligand binding are the discrimination between the “conformational selection model” and the “induced fit model”, and whether or not conformational changes lead to temperature dependent apparent binding heat capacities. The assessment of conformational changes associated with ligand binding by ITC is discussed. In addition, the “conformational selection” and “induced fit” models are reconciled, and discussed within the context of intrinsically (partially) unstructured proteins. Major conclusionsConformational equilibrium is a major contribution to binding heat capacity changes. A simple model may explain both conformational selection and induced fit scenarios. A temperature-independent binding heat capacity does not necessarily indicate absence of conformational changes upon ligand binding. ITC provides information on the energetics of conformational changes associated with ligand binding (and other possible additional coupled equilibria). General significancePreferential ligand binding to certain protein states leads to an equilibrium shift that is reflected in the coupling between ligand binding and additional equilibria. This represents the structural/energetic basis of the widespread dependence of ligand binding parameters on temperature, as well as pH, ionic strength and the concentration of other chemical species. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.

An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins

Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as -7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by -4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies.

Protein–protein binding affinity prediction on a diverse set of structures

Accurate binding free energy functions for protein-protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes. We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein-protein binding. The molecular descriptor set and descriptor values for all complexes are available in the Supplementary Material. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/~Affinity. paul.bates@cancer.org.uk. Supplementary data are available at Bioinformatics online.

Proline-based chiral stationary phases: A molecular dynamics study of the interfacial structure

Proline chains have generated considerable interest as a possible basis for new selectors in chiral chromatography. In this article, we employ molecular dynamics simulations to examine the interfacial structure of two diproline chiral selectors, one with a terminal trimethylacetyl group and one with a terminal t-butyl carbamate group. The solvents consist of a relatively apolar n-hexane/2-propanol and a polar water/methanol mixture. We begin with electronic structure calculations for the two chiral selectors to assess the energetics of conformational changes, particularly along the backbone where the amide bonds can alternate between cis and trans conformations. Force fields have been developed for the two selectors, based on these ab initio calculations. Molecular dynamics simulations of the selective interfaces are performed to examine the preferred backbone conformations, as a function of end-group and solvent. The full chiral surface includes the diproline selectors, trimethylsilyl end-caps, and silanol groups. Connection is made with selectivity measurements on these interfaces, where significant differences [1] are observed between these two very similar selectors.

The origins of sequence specificity of ethidium nucleic acid intercalation

The specificity of the intercalating dye ethidium for pyrimidine (3'-5') purine sequences in nucleic acid is studied. The known crystal structure of a complex of Iodo UpA with intercalated ethidium is utilized as a model for the binding. The energetics of the conformation changes from DNA-B to the intercalation geometry are examined for all possible dinucleotide pairs which could comprise the intercalation site. It is shown that differences in base-backbone interactions lead to sequence-dependent energetics of these conformational changes. Moreover, the calculated order of “unwinding” energies for different sites corresponds to the observed sequence isomer specificity for binding of ethidium to helical segments of nucleic acids. Thus the specificity appears to be largely a consequence of the different energetics of conformational changes within the nucleic acid sites. It is proposed that other intercalating molecules which require the same unwinding changes as ethidium will exhibit similar specificity.

λ‐Dynamics free energy simulation methods

Free energy calculations are fundamental to obtaining accurate theoretical estimates of many important biological phenomena including hydration energies, protein-ligand binding affinities and energetics of conformational changes. Unlike traditional free energy perturbation and thermodynamic integration methods, lambda-dynamics treats the conventional "lambda" as a dynamic variable in free energy simulations and simultaneously evaluates thermodynamic properties for multiple states in a single simulation. In the present article, we provide an overview of the theory of lambda-dynamics, including the use of biasing and restraining potentials to facilitate conformational sampling. We review how lambda-dynamics has been used to rapidly and reliably compute relative hydration free energies and binding affinities for series of ligands, to accurately identify crystallographically observed binding modes starting from incorrect orientations, and to model the effects of mutations upon protein stability. Finally, we suggest how lambda-dynamics may be extended to facilitate modeling efforts in structure-based drug design.

Conformational Dynamics Associated with Photodissociation of CO from Dehaloperoxidase Studied Using Photoacoustic Calorimetry

Herein, we present photoacoustic calorimetry and transient absorption studies of the dynamics and energetics associated with dissociation of a ligand from Fe(2+) dehaloperoxidase (DHP) from Amphitrite ornata. Our data show that CO photodissociation is associated with an endothermic (DeltaH = 8 +/- 3 kcal mol(-1)) volume expansion (DeltaV = 9.4 +/- 0.6 mL mol(-1)) that occurs within 50 ns upon photodissociation. No additional thermodynamics were detected on slower time scales (up to 10 micros), suggesting that the dissociated ligand rapidly escapes from the heme-binding pocket into the surrounding solvent. Similar volume and enthalpy changes were observed for CO photodissociation in the presence of the substrate, 2,4-dichlorophenol or 4-bromophenol, indicating that either the substrate does not bind in the protein distal cavity at ambient temperature or its presence does not impact the thermodynamic profile associated with ligand dissociation. We attribute a fast ligand exchange between the protein active site and the surrounding solvent to the high flexibility of the distal histidine residue, His55, that provides a direct pathway between the heme-binding pocket and the protein exterior. The dynamics and energetics of conformational changes observed for dissociation of a ligand from DHP differ significantly from those measured previously for photodissociation of CO from the structural homologue myoglobin, suggesting that structural dynamics in DHP are fine-tuned to enhance the peroxidase function of this protein.

Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin

Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

On the energetics of conformational changes and pH dependent redox behaviour of electron transfer proteins

Calculations of the electrostatic interaction energies for four metalloproteins that carry out electron transfer are reported. Each protein has a pH dependent redox potential from which the measured electrostatic interaction energy is obtained. The calculations were made using the X-ray structure coordinates and a semimacroscopic model of the interactions. For cytochrome c-551 and HIPIP the calculated and observed interaction energies were found to be approximately the same, in agreement with the fact that significant conformational changes do not accompany the ionisations. For cytochrome c 2 and azurin, however, major differences were found between the calculated and observed values. These are accounted for primarily by the occurrence of significant conformational changes accompanying the ionisations. The reorganisation energies for these conformational changes are ∼7.0 and ∼11.1 kJ·mol −1, respectively.