Biophysical Journal, Volume 87, Issue 1, 1 July 2004, Pages 92-104
Michèle Koenigsberger, Roger Sauser, Mathieu Lamboley, Jean-Louis Bény and Jean-Jacques Meister
Many experimental studies have shown that arterial smooth muscle cells respond with cytosolic calcium rises to vasoconstrictor stimulation. A low vasoconstrictor concentration gives rise to asynchronous spikes in the calcium concentration in a few cells (asynchronous flashing). With a greater vasoconstrictor concentration, the number of smooth muscle cells responding in this way increases (recruitment) and calcium oscillations may appear. These oscillations may eventually synchronize and generate arterial contraction and vasomotion. We show that these phenomena of recruitment and synchronization naturally emerge from a model of a population of smooth muscle cells coupled through their gap junctions. The effects of electrical, calcium, and inositol 1,4,5-trisphosphate coupling are studied. A weak calcium coupling is crucial to obtain a synchronization of calcium oscillations and the minimal required calcium permeability is deduced. Moreover, we note that an electrical coupling can generate oscillations, but also has a desynchronizing effect. Inositol 1,4,5-trisphosphate diffusion does not play an important role to achieve synchronization. Our model is validated by published in vitro experiments obtained on rat mesenteric arterial segments.
Biophysical Journal, Volume 90, Issue 3, 1 February 2006, Pages 864-877
Michael S. Lee and Mark A. Olson
A comparative analysis is provided of rigorous and approximate methods for calculating absolute binding affinities of two protein-ligand complexes: the FKBP protein bound with small molecules 4-hydroxy-2-butanone and FK506. Our rigorous approach is an umbrella sampling technique where a potential of mean force is determined by pulling the ligand out of the protein active site over several simulation windows. The results of this approach agree well with experimentally observed binding affinities. Also assessed is a commonly used approximate endpoint approach, which separately estimates enthalpy, solvation free energy, and entropy. We show that this endpoint approach has numerous variations, all of which are prone to critical shortcomings. For example, conventional harmonic and quasiharmonic entropy estimation procedures produce disparate results for the relatively simple protein-ligand systems studied in this work.
Abstract | Full Text | PDF (184 kb)
Biophysical Journal, Volume 95, Issue 10, 15 November 2008, Pages 4497-4511
Ben Cooke and Scott C. Schmidler
We describe a statistical approach to the validation and improvement of molecular dynamics simulations of macromolecules. We emphasize the use of molecular dynamics simulations to calculate thermodynamic quantities that may be compared to experimental measurements, and the use of a common set of energetic parameters across multiple distinct molecules. We briefly review relevant results from the theory of stochastic processes and discuss the monitoring of convergence to equilibrium, the obtaining of confidence intervals for summary statistics corresponding to measured quantities, and an approach to validation and improvement of simulations based on out-of-sample prediction. We apply these methods to replica exchange molecular dynamics simulations of a set of eight helical peptides under the AMBER potential using implicit solvent. We evaluate the ability of these simulations to quantitatively reproduce experimental helicity measurements obtained by circular dichroism. In addition, we introduce notions of statistical predictive estimation for force-field parameter refinement. We perform a sensitivity analysis to identify key parameters of the potential, and introduce Bayesian updating of these parameters. We demonstrate the effect of parameter updating applied to the internal dielectric constant parameter on the out-of-sample prediction accuracy as measured by cross-validation.
The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic effect in pathological conditions associated with these proteins. The most potent low molecular weight inhibitor of RNase reported to date is the compound 5′-phospho-2′-deoxyuridine-3-pyrophosphate (P→5)-adenosine-3-phosphate (pdUppA-3′-p). The 3′,5′-pyrophosphate group of this compound increases its affinity and introduces structural features which seem to be unique in pyrophosphate-containing ligands bound to RNase A, such as the adoption of a syn conformation by the adenosine base at RNase subsite B2 and the placement of the 5′-β-phosphate of the adenylate (instead of the α-phosphate) at subsite P1 where the phosphodiester bond cleavage occurs. In this work, we study by multi-ns molecular dynamics simulations the structural properties of RNase A complexes with the ligand pdUppA-3′-p and the related weaker inhibitor dUppA, which lacks the 3′ and 5′ terminal phosphate groups of pdUppA-3′-p. The simulations show that the adenylate 5′-β-phosphate binding position and the adenosine syn orientation constitute robust structural features in both complexes, stabilized by persistent interactions with specific active-site residues of subsites P1 and B2. The simulation structures are used in conjunction with a continuum-electrostatics (Poisson-Boltzmann) model, to evaluate the relative binding affinity of the two complexes. The computed relative affinity of pdUppA-3′-p varies between −7.9kcal/mol and −2.8kcal/mol for a range of protein/ligand dielectric constants (ϵp) 2–20, in good agreement with the experimental value (−3.6kcal/mol); the agreement becomes exact with ϵp=8. The success of the continuum-electrostatics model suggests that the differences in affinity of the two ligands originate mainly from electrostatic interactions. A residue decomposition of the electrostatic free energies shows that the terminal phosphate groups of pdUppA-3′-p make increased interactions with residues Lys7 and Lys66 of the more remote sites P2 and P0, and His119 of site P1.