Formation Of Encounter Complex Research Articles

Quantifying Crowding Effects on Transient Encounter Complex Formation during Protein Binding

Formation of transient encounter complexes during the early steps of protein binding is known to play an important role in the specific-complex formation by enhancing the association rate. The cellular medium is crowded with an ensemble of macromolecules, e.g., proteins, nucleic acids, sugars, lipids, etc. These macromolecules occupy the cell as high as 40% of its volume, thereby affecting the stability and speed of protein-protein interactions. We investigate the effects of macromolecular crowding on the formation of protein complexes, especially, encounter complexes, using a residue-based coarse-grained model for proteins and spherical macromolecular crowders. Crowders with solely repulsive interactions with protein(s) stabilize the formation of the native complex, while destabilizing most of the encounter complexes. However, certain encounter complexes, whose shapes are similar to that of the native complex, are shown to be stabilized by these repulsive crowders. On the other hand, attractive crowders exhibit the opposite trend, destabilizing the native complex and stabilizing the encounter complexes. The principal component analysis on the protein complexes shows that the free-energy landscape on the leading principal coordinates is affected by crowders, in which the energy barrier between the native complex and the dominant encounter complex is increased. We develop a theoretical model based on the scaled particle theory to quantify the crowding effects on the formation of encounter complexes. The newly developed theory can predict the effect of crowding accurately over a wide range of crowder sizes and interaction strengths between crowders and proteins. Our study provides the first (to our knowledge) theoretical description of crowding effects on the encounter complexes. We are currently extending its scope to provide microscopic understanding of the protein-protein interactions inside a cell.

Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study.

The industrial production of higher-generation semisynthetic cephalosporins starts from 7-aminocephalosporanic acid (7-ACA), which is obtained by deacylation of the naturally occurring antibiotic cephalosporin C (CephC). The enzymatic process in which CephC is directly converted into 7-ACA by a cephalosporin C acylase has attracted industrial interest because of the prospects of simplifying the process and reducing costs. We recently enhanced the catalytic efficiency on CephC of a glutaryl acylase from Pseudomonas N176 (named VAC) by a protein engineering approach and solved the crystal structures of wild-type VAC and the H57βS-H70βS VAC double variant. In the present work, experimental measurements on several CephC derivatives and six VAC variants were carried out, and the binding of ligands into the VAC active site was investigated at an atomistic level by means of molecular docking and molecular dynamics simulations and analyzed on the basis of the molecular geometry of encounter complex formation and protein-ligand potential of mean force profiles. The observed significant correlation between the experimental data and estimated binding energies highlights the predictive power of our computational method to identify the ligand binding mode. The present experimental-computational study is well-suited both to provide deep insight into the reaction mechanism of cephalosporin C acylase and to improve the efficiency of the corresponding industrial process.

Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges

We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex, which matches the crystal structure, features completely different interactions, namely the burial of the hydrophobic side chain of the peptide C-terminal residue and backbone hydrogen bonds. The simulations show that nonnative salt bridges stabilize kinetically the encounter complex during binding. Unbinding follows the inverse sequence of events with the same nonnative salt bridges in the encounter complex. Thus, in contrast to protein folding, which is driven by native interactions, the binding of charged peptides can be steered by nonnative interactions, which might be a general mechanism, e.g., in the recognition of histone tails by bromodomains.

WebSDA: a web server to simulate macromolecular diffusional association.

Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: ‘SDA docking’ to generate structures of the diffusional encounter complexes of two macromolecules, ‘SDA association’ to calculate bimolecular diffusional association rate constants, and ‘SDA multiple molecules’ to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/.

Correlation between excited-state intramolecular proton-transfer and singlet-oxygen quenching activities in 1-(acylamino)anthraquinones.

Excited-state intramolecular proton-transfer (ESIPT) and singlet-oxygen ((1)O2) quenching activities of intramolecularly hydrogen-bonded 1-(acylamino)anthraquinones have been studied by means of static and laser spectroscopies. The ESIPT shows a substituent effect, which can be explained in terms of the nodal-plane model. The ESIPT activity positively and linearly correlates with their (1)O2 quenching activity. The reason for this correlation can be understood by considering ESIPT-induced distortion of their ground-state potential surface and their encounter complex formation with (1)O2. Intramolecularly hydrogen-bonded hydroxyanthraquinones found in aloe also show a similar positive and linear correlation, which can be understood in the same way.

Role of electrostatic and hydrophobic interactions in the encounter complex formation of plastocyanin and cytochrome f

Role of electrostatic and hydrophobic interactions in the encounter complex formation of plastocyanin and cytochrome f

NMR Studies on Transient Protein Complexes: Perspectives

It is generally understood that protein-protein interactions proceed via transient encounter complexes that rapidly evolve into the functional stereospecific complex. Direct detection and characterization of the encounter complexes, however, been difficult due to their low population and short lifetimes. Recent application of NMR paramagnetic relaxation enhancement first visualized the structures of the encounter complex ensemble, and allowed the characterization of their physicochemical properties. Further, rational protein mutations that perturbed the encounter complex formation provided a clue to the target search pathway during protein-protein association. Understanding the structure and dynamics of encounter complexes will provide useful information on the mechanism of protein association.

Reduction Reaction of the Copper(II) Complex Bearing 1,3-Di(pyridine-2-carboxaldimino)propane (pitn) by Decamethylferrocene in Acetonitrile

The reduction reaction of the Cu(II)–pitn complex (pitn = 1,3-di(pyridine-2-carboxaldimino)propane) by decamethylferrocene [Fe(Cp*)2] was examined in acetonitrile. The observed pseudo-first-order rate constants exhibited saturation kinetics with increasing excess amount of [Fe(Cp*)2]. Detailed analyses revealed that the reaction is controlled by a structural change prior to the electron transfer step, rather than a conventional bimolecular electron transfer process preceded by ion pair (encounter complex) formation. The rate constant for the structural change was estimated to be 275 ± 13 s−1 at 298 K (∆H* = 33.3 ± 1.0 kJ·mol−1, ∆S* = 86 ± 5 J·mol−1·K−1), which is the fastest among gated reactions involving CuN4 complexes. It was confirmed by EPR measurement and Conflex calculations that the dihedral angle between the two N–N planes is significantly large (40°) in solution whereas it is merely 17.14° in the crystal.

Formation of transient protein complexes.

The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron transfer complexes. Here, we describe the current methods for studying and visualizing encounter complexes. We discuss recent developments in mapping the energy landscapes, the role of hydrophobic interactions during encounter complex formation and the discovery of futile encounter complexes. These studies have not only provided insight into encounter complexes of electron transfer proteins, but also opened up new questions and approaches for studying encounter complexes in other weakly associated proteins.

Atom depth analysis delineates mechanisms of protein intermolecular interactions

The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein–protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein–protein functional interactions.

Role of Hydrophobic Interactions in the Encounter Complex Formation of the Plastocyanin and Cytochrome f Complex Revealed by Paramagnetic NMR Spectroscopy

Protein complex formation is thought to be at least a two-step process, in which the active complex is preceded by the formation of an encounter complex. The interactions in the encounter complex are usually dominated by electrostatic forces, whereas the active complex is also stabilized by noncovalent short-range forces. Here, the complex of cytochrome f and plastocyanin, electron-transfer proteins involved in photosynthesis, was studied using paramagnetic relaxation NMR spectroscopy. Spin labels were attached to cytochrome f, and the relaxation enhancements of plastocyanin nuclei were measured, demonstrating that a large part of the cytochrome f surface area is sampled by plastocyanin. In contrast, plastocyanin is always oriented with its hydrophobic patch toward cytochrome f. The complex was visualized using ensemble docking, showing that the encounter complex is stabilized by hydrophobic as well as electrostatic interactions. The results suggest a model of electrostatic preorientation before the proteins make contact, followed by the formation of an encounter complex that rapidly leads to electron-transfer active conformations by gradual increase of the overlap of nonpolar surface areas on cytochrome f and plastocyanin. In this model the distinction between the encounter and active complexes vanishes, at least in the case of electron-transfer complexes, which do not require a high degree of specificity.

Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding

The catalytic events in members of the nucleotidylyl transferase superfamily are initiated by a millisecond binding of ATP in the active site. Through metadynamics simulations on a class I aminoacyl-tRNA synthetase (aaRSs), the largest group in the superfamily, we calculate the free energy landscape of ATP selection and binding. Mutagenesis studies and fluorescence spectroscopy validated the identification of the most populated intermediate states. The rapid first binding step involves formation of encounter complexes captured through a fly casting mechanism that acts upon the triphosphate moiety of ATP. In the slower nucleoside binding step, a conserved histidine in the HxxH motif orients the incoming ATP through base-stacking interactions resulting in a deep minimum in the free energy surface. Mutation of this histidine significantly decreases the binding affinity measured experimentally and computationally. The metadynamics simulations further reveal an intermediate quality control state that the synthetases and most likely other members of the superfamily use to select ATP over other nucleoside triphosphates.

Gaseous germyl cations: A theoretical investigation on the structure, properties, and mechanism of formation of [formula omitted] and [formula omitted] (n = 0–2)

The six germyl cations FnGe(OH)3-n+ and FnGe(NH2)3-n+ (n=0–2), recently observed in the gas phase from the cascade reactions between GeF3+ and H2O or NH3 (J. Mass Spectrom. 46 (2011) 465–477), were theoretically investigated by MP2 and CCSD(T) calculations. The bond distances and the electronic properties of these ions, and the stabilities of their complexes with H2O, NH3, and HF are regularly affected by the nature of the substituents. In particular, any Ge–X bond (X=F, OH, NH2) becomes progressively shorter by increasing the electronegativity of the two adjacent groups, and the most electronegative substituents produce also highest atomic charges at the Ge atom. In addition, replacing F with OH and NH2, the thermochemical stability of the cations substantially increases. This reflects in Lewis acidities of the F2Ge(X)+ and FGe(X)2+ (X=OH, NH2) which are invariably lower than GeF3+. The mechanisms of formation of the FnGe(OH)3-n+ and FnGe(NH2)3-n+ (n=0–2) were also investigated and found to be describable by the initial formation of encounter complexes between the reactant ions GeF3+, F2Ge(X)+ and FGe(X)2+ (X=OH, NH2) and H2O or NH3, which eventually dissociate into FnGe(OH)3-n+ and FnGe(NH2)3-n+ (n=0–2) and HF passing through two consecutive isomerizations.

Influence of Serum Proteins on Conformation of Prostate-Specific Antigen

Partition behavior of prostate-specific antigen (PSA) was studied in aqueous Dextran-Ficoll two-phase system. It was found that the partitioning of PSA changed in the presence of other proteins, in particular, bovine serum albumin, human serum albumin, human transferrin, and human gamma-globulin. The partition coefficient of PSA in mixtures with increasing amounts of these proteins decreased along the S-shaped curve and dropped to essentially the same value at the 104-105 protein: PSA molar ratio. Partition behavior of the above proteins was examined separately. Partition coefficient of a protein represents the protein solvent exposed residues; i.e., it reflects the 3D-structure of the protein in solution. Partition of binary protein mixtures reflects the interaction of the two proteins and therefore characterizes the PSA-induced conformational changes in a protein agent and the change in the PSA conformation induced by a protein agent. In other words, the protein effect on the partition behavior of free PSA may be explained by the effect of the non-specific PSA-protein interactions on PSA conformation. Formation of such PSA-protein encounter complexes was shown to be dominated by the electrostatic forces, since the efficiency of a given protein agent to induce changes in the partition behavior of PSA was proportional to its absolute mean net charge. Furthermore, in agreement with the earlier hypothesis that the protein segments with increased dynamic propensities (i.e., ‘discrete breathers’) can be important for conformational transitions accompanying binding processes, our analysis of intrinsically disordered regions (IDR) in all the proteins examined showed that the propensity for intrinsic disorder is related to the PSA partition-modulating capability of the protein.

The Kunitz 1 and Kunitz 3 domains of tissue factor pathway inhibitor are required for efficient inhibition of factor Xa

Tissue factor pathway inhibitor (TFPI) is a slow tight-binding inhibitor that inhibits factor (F)Xa in a biphasic fashion: a rapid formation of loose FXa·TFPI encounter complex is followed by slow rearrangement into a tight FXa·TFPI* complex in which the Kunitz-2 (K2) domain of TFPI binds and inhibits FXa. In the current study, full-length TFPI (TFPIfl) and various truncated TFPI constructs were used to assess the importance of TFPI domains other than K2 in the inhibition of FXa. In the absence of Ca2+ ions, FXa was more effectively inhibited by TFPIfl than Gla-domain less FXa. In turn, Ca2+ ions impaired FXa inhibition by TFPIfl but not by TFPI constructs that lack the C-terminus. This suggests that, in absence of Ca2+ ions, interactions between the C-terminus of TFPI and the Gla-domain of FXa promote FXa-inhibition. TFPIfl and K2K3 had similar efficiencies for encounter complex formation. However, K2K3 showed monophasic inhibition instead of biphasic inhibition, indicating absence of rearrangement into a tight complex. K1K2 and TFPI1-161 showed biphasic inhibition, but had less efficient encounter complex formation than TFPIfl. Finally, K2K3 was a 10-fold more efficient FXa- inhibitor than K2. These results indicate that K3-C-terminus enhances the formation of encounter complex and that K1 is required for isomerisation of the encounter- into tight complex. Since TFPIfl has a 10-fold higher Ki than K2K3-C-terminus, we propose that K1 is not only required for the transition of the loose to the tight FXa·TFPI* complex, but also inhibits FXa·TFPI encounter complex formation. This inhibitory activity is counteracted by K3 and C-terminus.

Mechanisms of Protein-Ligand Association and Its Modulation by Protein Mutations

Protein-ligand interactions are essential for nearly all biological processes, and yet the biophysical mechanism that enables potential binding partners to associate before specific binding occurs remains poorly understood. Fundamental questions include which factors influence the formation of protein-ligand encounter complexes, and whether designated association pathways exist. To address these questions, we developed a computational approach to systematically analyze the complete ensemble of association pathways. Here, we use this approach to study the binding of a phosphate ion to the Escherichia coli phosphate-binding protein. Various mutants of the protein are considered, and their effects on binding free-energy profiles, association rates, and association pathway distributions are quantified. The results reveal the existence of two anion attractors, i.e., regions that initially attract negatively charged particles and allow them to be efficiently screened for phosphate, which is subsequently specifically bound. Point mutations that affect the charge on these attractors modulate their attraction strength and speed up association to a factor of 10 of the diffusion limit, and thus change the association pathways of the phosphate ligand. It is demonstrated that a phosphate that prebinds to such an attractor neutralizes its attraction effect to the environment, making the simultaneous association of a second phosphate ion unlikely. This study suggests ways in which structural properties can be used to tune molecular association kinetics so as to optimize the efficiency of binding, and highlights the importance of kinetic properties.

Brownian dynamics simulation of substrate motion near active site of enzyme entrapped inside reverse micelle

Brownian dynamics simulation has been applied to analyze the influence of the electrostatic field of a reverse micelle on the enzyme-substrate complex formation inside a micelle. The probability that the enzyme-substrate complex will form from serine protease (trypsin) and the specific hydrophilic cationic substrate Nalpha-benzoyl-L: -arginine ethyl ester has been studied within the framework of the encounter complex formation theory. It has been shown that surfactant charge, dipole moments created by charged surfactant molecules and counterions, and permittivity of the inner core of reverse micelles can all be used as regulatory parameters to alter the substrate orientation near the active site of the enzyme and to change the probability that the enzyme-substrate complex will form.

Probing the Paracoccus denitrificans Cytochrome c1−Cytochrome c552 Interaction by Mutagenesis and Fast Kinetics

Electron transfer (ET) between Paracoccus denitrificans cytochrome (cyt) c(1) and cytochrome c(552) was studied using the soluble redox fragments cyt c(1CF) and cyt c(552F). A new ruthenium cyt c(552F) derivative labeled at C23 (Ru(z)-23-c(552F)) was designed to measure rapid electron transfer with cyt c(1CF) in the physiological direction using flash photolysis. The bimolecular rate constant k(12) decreased rapidly with ionic strength above 40 mM, consistent with a diffusional process guided by long-range electrostatic interactions between the two proteins. However, a new kinetic phase was detected at an ionic strength of <35 mM with the ruthenium photoexcitation technique in which k(12) became very rapid (3 x 10(9) M(-1) s(-1)) and nearly independent of ionic strength, suggesting that the reaction became so fast that it was controlled by short-range diffusion along the protein surfaces guided by hydrophobic interactions. These results are consistent with a two-step model for formation of the final encounter complex. No intracomplex electron transfer between Ru(z)-23-c(552F) and c(1CF) was observed even at the lowest ionic strength, indicating that the dissociation constant of the complex was >30 microM. On the other hand, the ruthenium-labeled yeast cytochrome c derivative Ru(z)-39-Cc formed a tight 1:1 complex with cyt c(1CF) at ionic strengths of <60 mM with an intracomplex electron transfer rate constant of 50000 s(-1). A group of cyt c(1CF) variants in the presumed docking site were generated on the basis of information from the yeast cyt bc(1)-cyt c cocrystal structure. Kinetic analysis of cyt c(1CF) mutants located near the heme crevice provided preliminary identification of the interaction site for cyt c(552F) and suggested that formation of the encounter complex is guided primarily by the overall electrostatic surface potential rather than by defined ions.

Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric, and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c-cytochrome c peroxidase, and p53:MDM2. In each case, proteins are modeled either as spherical particles, as dipolar spheres, or as collection of several small beads with one dipole. Spherical reaction patches are placed on the model proteins according to the known experimental structures of the protein complexes. In the computer simulations, concentration is varied by changing box size. Encounter is defined as overlap of the reaction patches and the corresponding first passage times are recorded together with the number of unsuccessful contacts before encounter. We find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20 to 9000. For all three models, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. Electrostatic steering enhances association up to 50-fold. If diffusional encounter is dominant (p53:MDM2) or similarly important as electrostatic steering (barnase:barstar), then encounter rate decreases with decreasing patch radius. More detailed modeling of protein shapes decreases encounter rates by 5%-95%. Our study shows how generic principles of protein-protein association are modulated by molecular features of the systems under consideration. Moreover it allows us to assess different coarse-graining strategies for the future modeling of the dynamics of large protein complexes.

A mechanistic study of ferrioxamine B reduction by the biological reducing agent ascorbate in the presence of an iron(II) chelator

The iron overload drug desferal (desferrioxamine B) forms the stable iron complex ferrioxamine B. The reduction potential of ferrioxamine B ( E o = −482 mV versus NHE pH 7) prohibits its reduction by biological reducing agents such as ascorbate, but it was found that the iron(II) chelator 2,2′-bipyridine (bipy) facilitates this reduction. Evidence is given to support the formation of a ternary complex between iron, bipy, and desferrioxamine B as the key step in facilitating the reduction. The equilibrium constant for the formation of the ternary complex was found to be 8.9 × 10 7 and ternary complex formation is explained in terms of a three step mechanism. The mechanism for the reduction of ferrioxamine B is discussed in terms of rapidly established pre-equilibria which include ternary complex formation, ascorbic acid deprotonation, and encounter complex formation between ascorbate and the ternary complex. These equilibria are followed by rate limiting reduction of the ternary complex. Bipy was found to be a similar facilitator to sulfonated bathophenanthroline for the reduction of ferrioxamine B by ascorbate.