Temperature-enhanced association of proteins due to electrostatic interaction: a coarse-grained simulation of actin-myosin binding

Association of protein molecules constitutes the basis for the interaction network in a cell. Despite its fundamental importance, the thermodynamic aspect of protein-protein binding, particularly the issues relating to the entropy change upon binding, remains elusive. The binding of actin and myosin, which are vital proteins in motility, is a typical example, in which two different binding mechanisms have been argued: the binding affinity increases with increasing temperature and with decreasing salt-concentration, indicating the entropy-driven binding and the enthalpy-driven binding, respectively. How can these thermodynamically different binding mechanisms coexist? To address this question, which is of general importance in understanding protein-protein bindings, we conducted an in silico titration of the actin-myosin system by molecular dynamics simulation using a residue-level coarse-grained model, with particular focus on the role of the electrostatic interaction. We found a good agreement between in silico and in vitro experiments on the salt-concentration dependence and the temperature dependence of the binding affinity. We then figured out how the two binding mechanisms can coexist: the enthalpy (due to electrostatic interaction between actin and myosin) provides the basal binding affinity, and the entropy (due to the orientational disorder of water molecules) enhances it at higher temperatures. In addition, we analyzed the actin-myosin complex structures observed during the simulation and obtained a variety of weak-binding complex structures, among which were found an unusual binding mode suggested by an earlier experiment and precursor structures of the strong-binding complex proposed by electron microscopy. These results collectively indicate the potential capability of a residue-level coarse-grained model to simulate the association-dissociation dynamics (particularly for transient weak-bindings) exhibited by larger and more complicated systems, as in a cell.     

Steric vs. electrostatic effects in the nucleophilic addition to a hindered cyclohexanone

The relative importance of steric vs. electrostatic effects in the nucleophilic addition to (4R,6S)-4-(tert-butyldimethylsiloxy)-2,2,6-trimethylcyclohexanone (1), a well-known chiral building block, is investigated.     

Steric and electrostatic interactions in hexacyclic ring systems: The origin of the buttressing effect

Ring deformation in a number of 2-trichloromethyl-1,3-dioxanes could be traced in their ¹H NMR spectra from anomalies in coupling constants. No distortion occurs when the 2-substituent is a dichloromethyl or a tertiobutyl group, or when a 4-axial substituent is lacking. It was impossible to deduce the ring geometry from the vicinal coupling constants, but the nature of the ring deformation has been ascertained by NMR data (³J_exo, Δδ) and dipole moment calculations. Flexible conformations are not the origin of the observed anomalies. The rotomeric populations in 2-dichloromethyl-1,3-dioxanes has been evaluated and the origin of the buttressing effect, as caused by different substitution, has been disclosed.     

Liquid-liquid interfaces: In isolation and in interaction

Although liquid-liquid interfaces are as important as liquid-vapor interfaces in many fields, including biology and technology, they have received much less attention in terms of systematic experimental studies. Many techniques are, in principle, relevant to both types of interface; likewise similar theories can often be developed for both. The basic physical chemistry of isolated interfaces, i.e. interfaces between two bulk liquids in mutual contact, is introduced first in this review. The interfacial tension, the forces acting at interfaces (i.e. van der Waals, Coulombic and steric forces), and the thermodynamic treatment of such systems are each considered, and the experimental techniques and some of the more important results are summarized. Next, the problem of three-phase contact (in which two or three of the phases are liquid) is introduced, and the concept of wetting and spreading considered. This leads to a discussion of systems in which two bulk phases (either, or both, of which are liquids) are separated by a liquid film; the mutual interaction of the two interfaces now becomes relevant. The stability of such systems is discussed in terms of the various forces acting within the systems, plus any external forces, such as gravity. The thermodynamics of liquid films is briefly introduced, and some discussion of the magnitude of the two interfacial tensions given. Finally, it is shown that the factors governing the formation and stability of liquid droplets and emulsion systems are directly related to the consideration of the earlier sections.     

Contributions to reversed-phase column selectivity. I. Steric interaction

In reversed-phase chromatography (RPC), the restricted retention of "bulky" solutes can occur in one of two ways, giving rise to either "shape selectivity" or "steric interaction." Starting with data for 150 solutes and 167 monomeric type-B alkylsilica columns, the present study examines the steric interaction process further and compares it with shape selectivity. The dependence of column hydrophobicity and steric interaction on column properties (ligand length and concentration, pore diameter, end-capping) was determined and compared. The role of the solute in steric interaction was found to be primarily a function of solute molecular length, with longer solutes giving increased steric interaction. We find that there are several distinct differences in the way shape selectivity and steric interaction are affected by separation conditions and the nature of the sample. Of particular interest, steric interaction exhibits a maximum effect for monomeric C(18) columns, and becomes less important for either a C(1) or C(30) column; shape selectivity appears unimportant for monomeric C(1)-C(18) columns at ambient and higher temperatures, but becomes pronounced for C(30) - as well as polymeric columns with ligands ≥C(8). One hypothesis is that shape selectivity involves the presence or creation of cavities within the stationary phase that can accommodate a retained solute (a primarily enthalpic process), while steric interaction mainly makes greater use of spaces that pre-exist the retention of the solute (a primarily entropic process). The related dependence of hydrophobic interaction on column properties was also examined.     

Steric control of bacteriochlorophyll ligation

The axial coordination of central Mg(2+) ion in chlorophylls is of great structural and functional importance for virtually all photosynthetic chlorophyll proteins; however, little thermodynamic data are available on the ligand binding to these pigments. In the present study, spectral deconvolution of the bacteriochlorophyll Q(X) band serves to determine the ligand binding equilibria and relationships between thermodynamic parameters of ligand binding, ligand properties, and steric interactions occurring within the pigment. On the basis of the temperature effects on coordination, DeltaH degrees, DeltaS degrees, and DeltaG degrees of binding various types of ligands (acetone, dimethylformamide, imidazole, and pyridine) to diastereoisomeric bacteriochlorophylls were derived from respective van't Hoff's plots. At ambient temperatures, only ligation by imidazole and pyridine occurs spontaneously while DeltaG degrees becomes positive for ligation by acetone and dimethylformamide, due to a relatively large entropic effect, which is dominating when the energetic effects of ligation are small. It reflects, in quantitative terms, the control of the equatorial coordination of the Mg(2+) ion via the axial coordination: a "hard" free Mg(2+) ion is made into a softer center through the coordination of tetrapyrrole. Pigment structural features have comparable effects on the energetic and entropic contributions to the difference of ligation free energy between the diastereoisomers of bacteriochlorophyll. DeltaS degrees and DeltaH degrees values are consistently lower for the S epimer, most likely due to the steric crowding between bulky substituents. The two epimers show a 5 J.mol(-1).K(-1) difference in DeltaS degrees values, regardless of the ligand type, while the difference in DeltaH degrees amounts to 1.7 kJ.mol(-1), depending on the ligand. Such steric control of ligation would relate to the partial diastereoselectivity of chlorophyll self-assembly and, in particular, the very high diastereoselectivity of the ligation of chlorophylls in photosynthetic proteins.     

Steric and electrostatic effects in dye-cellulose interactions by the MTD and CoMFA approaches

This paper presents the application of the MTD (minimal steric difference) analysis and CoMFA (comparative molecular field analysis) to series of anthraquinone vat, mono and disazo and disperses dyes with known affinities for cellulose fiber. A comparison of the results demonstrates that these methods usually agree with the prediction of structural features favorable for dyeing. A series of n = 49 anthraquinone vat dyes was studied by MTD with r2 between 0.903 and 0.941 and r2CV values in the range of 0.827-0.878. For CoMFA, r2 = 0.992, r2CV = 0.841 were obtained; the CoMFA field is in rather good agreement with vertex attributions, by MTD for attractive and repulsive vertices. Anionic disazo dyes were studied by the CoMFA method (n = 21, r2 = 0.999, r2CV = 0.703). Monoazo dyes (several series) were studied by CoMFA and MTD. The effect of lipophilicity on dye fiber affinity was, also, studied for these dyes. Disperse dye adsorption was analyzed by MTD and CoMFA (n = 27, r2 = 0.925, r2CV = 0.776). Conclusions refer to the effect of structural features of dye molecules upon adsorption on cellulose fibers.     

Steric and electrostatic effects in dye-cellulose interactions by the MTD and CoMFA approaches

This paper presents the application of the MTD (minimal steric difference) analysis and CoMFA (comparative molecular field analysis) to series of anthraquinone vat, mono and disazo and disperses dyes with known affinities for cellulose fiber. A comparison of the results demonstrates that these methods usually agree with the prediction of structural features favorable for dyeing. A series of n =49 anthraquinone vat dyes was studied by MTD with r 2 between 0.903 and 0.941 and r CV 2 values in the range of 0.827-0.878. For CoMFA, r 2 =0.992, r CV 2 =0.841 were obtained; the CoMFA field is in rather good agreement with vertex attributions, by MTD for attractive and repulsive vertices. Anionic disazo dyes were studied by the CoMFA method ( n =21, r 2 =0.999, r CV 2 =0.703). Monoazo dyes (several series) were studied by CoMFA and MTD. The effect of lipophilicity on dye fiber affinity was, also, studied for these dyes. Disperse dye adsorption was analyzed by MTD and CoMFA ( n =27, r 2 =0.925, r CV 2 =0.776). Conclusions refer to the effect of structural features of dye molecules upon adsorption on cellulose fibers.     

Hydroxide-ion binding to nonionic interfaces in aqueous solution

The mechanism of hydroxide ion binding to nonionic surfaces is explored by variation of the properties of the water-aggregate interface and by variation of the type of the aggregate.     

Local orientations of fluctuating fluid interfaces

Thermal fluctuations cause the local normal vectors of fluid interfaces to deviate from the vertical direction defined by the flat mean interface position. This leads to a nonzero mean value of the corresponding polar tilt angle which renders a characterization of the thermal state of an interface. Based on the concept of an effective interface Hamiltonian we determine the variances of the local interface position and of its lateral derivatives. This leads to the probability distribution functions for the metric of the interface and for the tilt angle which allows us to calculate its mean value and its mean-square deviation. We compare the temperature dependences of these quantities as predicted by the simple capillary-wave model, by an improved phenomenological model, and by the microscopic effective interface Hamiltonian derived from density-functional theory. The mean tilt angle discriminates clearly between these theoretical approaches and emphasizes the importance of the variation of the surface tension at small wavelengths. Also the tilt angle two-point correlation function is determined which renders an additional structural characterization of interfacial fluctuations. Various experimental accesses to measure the local orientational fluctuations are discussed.     

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method

Molecular dynamics (MD) simulations of heptane/vapor, hexadecane/vapor, water/vapor, hexadecane/water, and dipalmitoylphosphatidylcholine (DPPC) bilayers and monolayers are analyzed to determine the accuracy of treating long-range interactions in interfaces with the isotropic periodic sum (IPS) method. The method and cutoff (rc) dependences of surface tensions, density profiles, water dipole orientation, and electrostatic potential profiles are used as metrics. The water/vapor, heptane/vapor, and hexadecane/vapor interfaces are accurately and efficiently calculated with 2D IPS (rc=10 A). It is demonstrated that 3D IPS is not practical for any of the interfacial systems studied. However, the hybrid method PME/IPS [Particle Mesh Ewald for electrostatics and 3D IPS for Lennard-Jones (LJ) interactions] provides an efficient way to include both types of long-range forces in simulations of large liquid/vacuum and all liquid/liquid interfaces, including lipid monolayers and bilayers. A previously published pressure-based long-range LJ correction yields results similar to those of PME/IPS for liquid/liquid interfaces. The contributions to surface tension of LJ terms arising from interactions beyond 10 A range from 13 dyn/cm for the hexadecane/vapor interface to approximately 3 dyn/cm for hexadecane/water and DPPC bilayers and monolayers. Surface tensions of alkane/vapor, hexadecane/water, and DPPC monolayers based on the CHARMM lipid force fields agree very well with experiment, whereas surface tensions of the TIP3P and TIP4P-Ew water models underestimate experiment by 16 and 11 dyn/cm, respectively. Dipole potential drops (DeltaPsi) are less sensitive to long-range LJ interactions than surface tensions. However, DeltaPsi for the DPPC bilayer (845+/-3 mV proceeding from water to lipid) and water (547+/-2 mV for TIP4P-Ew and 521+/-3 mV for TIP3P) overestimate experiment by factors of 3 and 5, respectively, and represent expected deficiencies in nonpolarizable force fields.     

DelPhiForce,a tool for electrostatic force calculations: Applications to macromolecular binding

Long‐range electrostatic forces play an important role in molecular biology, particularly in macromolecular interactions. However, calculating the electrostatic forces for irregularly shaped molecules immersed in water is a difficult task. Here, we report a new tool, DelPhiForce, which is a tool in the DelPhi package that calculates and visualizes the electrostatic forces in biomolecular systems. In parallel, the DelPhi algorithm for modeling electrostatic potential at user‐defined positions has been enhanced to include triquadratic and tricubic interpolation methods. The tricubic interpolation method has been tested against analytical solutions and it has been demonstrated that the corresponding errors are negligibly small at resolution 4 grids/Å. The DelPhiForce is further applied in the study of forces acting between partners of three protein–protein complexes. It has been demonstrated that electrostatic forces play a dual role by steering binding partners (so that the partners recognize their native interfaces) and exerting an electrostatic torque (if the mutual orientations of the partners are not native‐like). The output of DelPhiForce is in a format that VMD can read and visualize, and provides additional options for analysis of protein–protein binding. DelPhiForce is available for download from the DelPhi webpage at http://compbio.clemson.edu/downloadDir/delphiforce.tar.gz © 2017 Wiley Periodicals, Inc.     

Steric stabilization of polyvinyl alcohol adsorbed on silica/water and water/oil interfaces

The steric hindrance of various polyvinyl alcohol samples was investigated by measuring the force-distance curves between crossed quartz filaments with adsorbed layers of PVA. Results were obtained by changing the concentration of macromolecules, the average macromolecular weight, the electrolyte concentration, the kind of electrolytes, the temperature and by adding organic solvents. The results were compared with calculations using the Hesselink-Vrij-Overbeek Theory.It could be shown that only a small amount of “longer” tails is responsible for the stabilization but the segment distribution functions are different for different samples.     

Local electrochemical impedance spectroscopy: A window into heterogeneous interfaces

The ability to probe surface reactivity on a local scale has led to a new insight into the comprehension of the electrochemical reactivity in relation with the microstructure of the surface. Among the different techniques developed in recent years, local electrochemical impedance spectroscopy has the advantage of using a transient approach to locally characterize a stationary electrochemical system without the need to add any redox mediator in solution, which is a great advantage for the study of different systems.In this review, particular attention is paid to the different ways of measuring the local impedance, and the technique implementing a local current measurement in solution is deeply discussed. This local electrochemical impedance spectroscopy journey also encompasses a discussion about technical and experimental limitations.     

Electric double layer and electrostatic interaction of hydrophobic particles

An hypothesis regarding the impact of water density near hydrophobic surfaces on the electrostatic component of their interaction was offered. A theoretical model of the electric double layer and the interparticle interaction under conditions of the variable density and, consequently, variable dielectric permittivity of water has been developed. It was shown that reduction of the dielectric permittivity near interfaces determined by their hydrophobicity resulted in compression of double electrical layers and weakening of their overlapping. This, in its turn, results in reduction of the electrostatic repulsion of hydrophobic disperse particles as compared with nonhydrophobic ones.     

Approximate exchange and electrostatic interaction energies of deformed ions

Computation of exchange-polarization and electrostatic-polarization interaction energies between ions is the most expensive step in ab initio investigations of the properties of perfect and imperfect ionic crystals. In the present paper approximate formulas are proposed for these quantities. They save about 95% of the computation time and give these values with an error less than 0.2 kcal mol^?1 as compared to ab initio results. The formulas for the exchange- and electrostatic-polarization energies involve the generalized overlap integral between the one-determinantal wave functions of the deformed ions. The approximations are tested in the calculations of the interactions of deformed ions in LiF and NaF crystals.     

Local control of protein binding and cell adhesion by patterned organic thin films

Control of the cell adhesion and growth on chemically patterned surfaces is important in an increasing number of applications in biotechnology and medicine, for example implants, in-vitro cellular assays, and biochips. This review covers patterning techniques for organic thin films suitable for site-directed guidance of cell adhesion to surfaces. Available surface patterning techniques are critically evaluated, with special emphasis on surface chemistry that can be switched in time and space during cultivation of cells. Examples from the authors’ laboratory include the use of cell-repellent self-assembled monolayers (SAM) terminated by oligoethylene glycol (OEG) units and the lifting of the cell repellent properties by use of electrogenerated Br₂/HOBr which can be performed with positionable microelectrodes. Structural changes of the SAM were analyzed by polarization-modulated infrared reflection absorption spectroscopy (PM IRRAS). Use of a soft array system of individually addressable microelectrodes enables formation of flexible and complex patterns in a short time and has the potential for further acceleration of probe-induced local manipulation of cell adhesion.     

Steric control over arene coordination to beta-diiminate rhodium(I) fragments

The bulky ligands L(X)- (L(X) = (2,6-C6H3X2)NC(Me)CHC(Me)N(2,6-C6H3X2), X =Cl, Me) can be used to generate fluxional mononuclear arene complexes [L(X)Rh(eta4-arene)] (arene = benzene, toluene, m-xylene, mesitylene), which for X = Me disproportionate to fluxional dinuclear complexes [[L(Me)Rh]2(anti-mu-arene)]. For both mononuclear and dinuclear complexes, steric interactions do not stop the fluxionality but govern the preferred orientation of the methyl-substituted arenes, thus allowing indirect determination of the static NMR parameters. For the mu-arene complexes, two distinct types of fluxionality are proposed on the basis of calculations: ring rotation and metal shift. In the solid state, the toluene complex has an eta4(1,2,3,4):eta4(3,4,5,6)-bridged structure; the NMR analysis indicates that the benzene and m-xylene complexes have similar structures. The mesitylene complex, however, has an unprecedented eta3(1,2,3):eta3(3,4,5)-bridged structure, which is proposed to correspond to the transition state for arene rotation in the other cases. Steric factors are thought to be responsible for this reversal of stabilities.