Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.

Macromolecular crowding inside cells affects the thermodynamic and kinetic properties of proteins. The scaled particle theory (SPT) has played an important role toward establishing a qualitative picture for the effects of crowding. However, SPT-based modeling lacks molecular details.

From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions.

In receptor-ligand binding, a question that generated considerable interest is whether the mechanism is induced fit or conformational selection. This question is addressed here by a solvable model, in which a receptor undergoes transitions between active and inactive forms. The inactive form is favored while unbound but the active form is favored while a ligand is loosely bound.

Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins.

Ca(2+ )binding proteins are essential for regulating the role of Ca(2+ )in cell signaling and maintaining Ca(2+ )homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca(2+ )binding proteins and are known to influence Ca(2+ )binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca(2+ )binding and protein stability using de novo designed Ca(2+ )binding proteins.

The gates of ion channels and enzymes.

Protein dynamics are essential for virtually all protein functions, certainly for gating mechanisms of ion channels and regulation of enzyme catalysis. Ion channels usually feature a gate in the channel pore that prevents ion permeation in the closed state. Some bifunctional enzymes with two distant active sites use a tunnel to transport intermediate products; a gate can help prevent premature leakage.

Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences.

Macromolecular crowding has long been known to significantly affect protein oligomerization, and yet no direct quantitative measurements appear to have been made of its effects on the binding free energy of the elemental step of adding a single subunit. Here, we report the effects of two crowding agents on the binding free energy of two subunits in the Escherichia coli polymerase III holoenzyme. The crowding agents are found, paradoxically, to have only a modest stabilizing effect, of the order of 1 kcal/mol, on the binding of the two subunits.

Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability.

Theoretical models predict that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different.

Nonadditive effects of mixed crowding on protein stability.

The crowded environments inside cells can have significant effects on the folding stability and other biophysical properties of proteins. In this study on how macromolecular crowding affects protein folding, we took a significant step toward realistically mimicking intracellular environments by using a mixture of two crowding agents, Ficoll and dextran. We found that the mixed crowding exerts a greater stabilizing effect than the sum of the two individual crowding agents.

Dissection of the high rate constant for the binding of a ribotoxin to the ribosome.

Restrictocin belongs to a family of site-specific ribonucleases that kill cells by inactivating the ribosome. The restrictocin-ribosome binding rate constant was observed to exceed 10(10) M(-1) s(-1). We have developed a transient-complex theory to model the binding rates of protein-protein and protein-RNA complexes.

Crowding effects of membrane proteins.

In cell membranes, membrane proteins occupy approximately 30% of the total surface area. Crowding effects similar to those in the solution phase are thus to be expected. In addition, there are crowding effects unique to proteins bound to the two-dimensional membranes, such as those exerted on the equilibration of a protein between two membrane orientations and on the redistribution of proteins between different locations in a cell membrane.

Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method.

The Poisson-Boltzmann (PB) equation is widely used for modeling solvation effects. The computational cost of PB has restricted its applications largely to single-conformation calculations. The generalized Born (GB) model provides an approximation at substantially reduced cost.

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences.

Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion, are discussed.

Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibition.

Nicotinic AChRs (nAChRs) represent a paradigm for ligand-gated ion channels. Despite intensive studies over many years, our understanding of the mechanisms of activation and inhibition for nAChRs is still incomplete. Here, we present molecular dynamics (MD) simulations of the alpha7 nAChR ligand-binding domain, both in apo form and in alpha-Cobratoxin-bound form, starting from the respective homology models built on crystal structures of the acetylcholine-binding protein.

Prediction of protein solubility from calculation of transfer free energy.

Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water.

Effect of mixed macromolecular crowding agents on protein folding.

In cells, proteins fold and unfold in the presence of macromolecules with various sizes and shapes. Recent experiments by Liang and coworkers (J Biol Chem 2004;279:55109-55116; J Mol Biol 2006;364:469-482) show that protein refolding is enhanced by a mixture of two different crowding agents relative to the individual crowding agents and an optimal mixing ratio exists. Here, we present a theory that predicts the existence of an optimal mixing ratio.

A minimum-reaction-flux solution to master-equation models of protein folding.

Master equations are widely used for modeling protein folding. Here an approximate solution to such master equations is presented. The approach used may be viewed as a discrete variational transition-state theory.

Protein association with circular DNA: rate enhancement by nonspecific binding.

An analytical solution for the nonspecific-binding-facilitated diffusion-controlled rate of association of a protein with a specific site on a circular DNA is derived. Nonspecific binding is modeled by a short-range attractive surface potential. The protein undergoes diffusion in the bulk solution and in the surface layer.

Calculation of free-energy differences and potentials of mean force by a multi-energy gap method.

A method is proposed to significantly accelerate the convergence of free-energy calculations. It introduces a bias factor in Monte Carlo simulations or, equivalently, a bias force in molecular dynamics simulations. The bias factor targets the energy gap, i.

On the Dielectric Boundary in Poisson-Boltzmann Calculations.

In applying the Poisson-Boltzmann (PB) equation for calculating the electrostatic free energies of solute molecules, an open question is how to specify the boundary between the low-dielectric solute and the high-dielectric solvent. Two common specifications of the dielectric boundary, as the molecular surface (MS) or the van der Waals (vdW) surface of the solute, give very different results for the electrostatic free energy of the solute. With the same atomic radii, the solute is more solvent-exposed in the vdW specification.

Helix formation inside a nanotube: possible influence of backbone-water hydrogen bonding by the confining surface through modulation of water activity.

Recent molecular dynamics simulations of Sorin and Pande [J. Am. Chem.

Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.

We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA.

Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible.

The prediction of salt-mediated electrostatic effects with high accuracy is highly desirable since many biological processes where biomolecules such as peptides and proteins are key players can be modulated by adjusting the salt concentration of the cellular milieu. With this goal in mind, we present a novel implicit-solvent based linear Poisson-Boltzmann (PB) solver that provides very accurate nonspecific salt-dependent electrostatic properties of biomolecular systems. To solve the linear PB equation by the Monte Carlo method, we use information from the simulation of random walks in the physical space.

GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.

The nonlinear Poisson-Boltzmann (NLPB) equation can provide accurate modeling of electrostatic effects for nucleic acids and highly charged proteins. Generalized Born methods have been developed to mimic the linearized Poisson-Boltzmann (LPB) equation at substantially reduced cost. The computer time for solving the NLPB equation is approximately fivefold longer than for the LPB equation, thus presenting an even greater obstacle.

GBr(6): a parameterization-free, accurate, analytical generalized born method.

The Poisson-Boltzmann (PB) equation is widely used for modeling electrostatic effects and solvation for macromolecules. The generalized Born (GB) model has been developed to mimic PB results at substantial lower computational cost. Here, we report an analytical GB method that reproduces PB results with high accuracy.