Recent development and application of constant pH molecular dynamics.

Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique.

Predicting proton titration in cationic micelle and bilayer environments.

Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pKa's in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pKa of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge.

Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles.

Stimuli-responsive, self-assembling nanomaterials hold a great promise to revolutionize medicine and technology. However, current discovery is slow and often serendipitous. Here we report a multiscale modeling study to elucidate the pH-controlled self-assembly of nanofibers from the peptide amphiphiles, palmitoyl-I-AE-NH.

Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.

Recent interest in the development of surfactant-based nanodelivery systems targeting tumor sites has sparked our curiosity in understanding the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Toward this goal, we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study the de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20-30% ionization and being completed at 50%.

Introducing titratable water to all-atom molecular dynamics at constant pH.

Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the new method in replica-exchange continuous constant pH molecular dynamics simulations of three proteins, HP36, BBL, and HEWL.

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.

Detailed knowledge of the self-assembly and phase behavior of pH-sensitive surfactants has implications in areas such as targeted drug delivery. Here we present a study of the formation of micelle and bilayer from lauric acids using a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with conformational sampling in explicit solvent and the pH-based replica-exchange protocol. We find that at high pH conditions a spherical micelle is formed, while at low pH conditions a bilayer is formed with a considerable degree of interdigitation.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation.

Diarylcyclopentendione metabolite obtained from a Preussia typharum isolate procured using an unconventional cultivation approach.

An uncommon 2,5-diarylcyclopentenone compound, preussidone (1), and a new biphenyl compound, 1',5-dimethoxy-3,5'-dimethyl-2,3'-oxybiphenyl-1,2'-diol (4), together with two known biphenyl compounds, 5-methoxy-3,5'-dimethyl-2,3'-oxybiphenyl-1,1',2'-triol (2) and cyperin (3), were obtained from a Preussia typharum isolate that was procured using a panel of unconventional media formulations. The structures of the new compounds were established by NMR and mass spectrometry, while the absolute configuration of 1 was assigned by quantum chemical ECD and VCD calculations. The antimicrobial and DPPH radical scavenging activities of 1-4 were tested.

Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins.

When the major ampulate spidroins (MaSp1) are called upon to form spider dragline silk, one of nature's most amazing materials, a small drop in pH must occur. Using a state-of-the-art simulation technique, constant pH molecular dynamics, we discovered a few residues that respond to the pH signal in the dimerization of the N-terminal domain (NTD) of MaSp1 which is an integral step in the fiber assembly. At neutral pH the deprotonation of Glu79 and Glu119 leads to water penetration and structural changes at the monomer-monomer binding interface.

Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton.

The coupling of two NO molecules catalyzed by iron porphyrins is of biological importance. We use density functional theory calculations to examine the factors that control the fundamental N-N bond formation step mediated by a single iron porphyrin. The presence of an axial Im ligand, extra electrons, and most importantly a proton, enhance the N-N bond formation step in our model.

Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits.

Resistance mutations to antibiotics targeting rRNA can be far from the drug-binding site. Crystallography studies revealed that the antibiotic resistance mutation G2482A (G2447A in E. coli ) in Haloarcula marismortui 50S ribosomes does not directly contact the drug or introduce changes to the ribosomal structure except for losing a potassium ion coordinated to a base triple at the drug-binding site.

Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.

Ionization-coupled conformational phenomena are ubiquitous in biology. However, quantitative characterization of the underlying thermodynamic cycle comprised of protonation and conformational equilibria has remained an elusive goal. Here we use theory and continuous constant pH molecular dynamics (CpHMD) simulations to provide a thermodynamic description for the coupling of proton titration and conformational exchange between two distinct states of a protein.

Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles.

Calculation of surfactant pK(a)'s in micelles is a challenging task using traditional electrostatic methods due to the lack of structural data and information regarding the effective dielectric constant. Here we test the implicit- and hybrid-solvent-based continuous constant pH molecular dynamics (CpHMD) methods for predicting the pK(a) shift of a lauric acid solubilized in three micelles: dodecyl sulfate (DS), dodecyltrimethylammonium (DTA), and dodecyltriethylene glycol ether (DE3). Both types of simulations are able to reproduce the observed positive pK(a) shifts for the anionic DS and nonionic DE3 micelles.

Progress in the prediction of pKa values in proteins.

The pK(a) -cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK(a) values and protein electrostatics in general. The first round of the pK(a) -cooperative, which challenged computational labs to carry out blind predictions against pK(a) s experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6-10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics.

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.

A computational tool that offers accurate pKa values and atomically detailed knowledge of protonation-coupled conformational dynamics is valuable for elucidating mechanisms of energy transduction processes in biology, such as enzyme catalysis and electron transfer as well as proton and drug transport. Toward this goal we present a new technique of embedding continuous constant pH molecular dynamics within an explicit-solvent representation. In this technique we make use of the efficiency of the generalized-Born (GB) implicit-solvent model for estimating the free energy of protein solvation while propagating conformational dynamics using the more accurate explicit-solvent model.

Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions.

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.

In recent years, all-atom and coarse-grained models have been developed and applied to simulations of micelles and biological membranes. Here, we explore the question of whether a combined all-atom representation of surfactant molecules and continuum description of solvent based on the generalized Born model can be used to study surfactant micelles. Specifically, we report the parameterization of the GBSW model with a surface-area dependent nonpolar solvation energy term for dodecyl sulfate, dodecyl tetramethylammonium, and dodecyl triethyleneglycol ether molecules.

Uncovering specific electrostatic interactions in the denatured states of proteins.

The stability and folding of proteins are modulated by energetically significant interactions in the denatured state that is in equilibrium with the native state. These interactions remain largely invisible to current experimental techniques, however, due to the sparse population and conformational heterogeneity of the denatured-state ensemble under folding conditions. Molecular dynamics simulations using physics-based force fields can in principle offer atomistic details of the denatured state.

Probing the strand orientation and registry alignment in the propagation of amyloid fibrils.

Detailed knowledge of the structure and growth mechanism of amyloid fibrils is important for understanding the disease process. Recently, solid-state NMR and other spectroscopic data have revealed the equilibrium organization of the tertiary structure of fibrils formed by various segments of beta-amyloid peptides. A three-step "dock-and-lock" mechanism for fibril growth has been proposed on the basis of the kinetic data.

A method to determine residue-specific unfolded-state pKa values from analysis of stability changes in single mutant cycles.

It is now widely recognized that the unfolded state of a protein in equilibrium with the native state under folding conditions may contain significant residual structures. However, due to technical difficulties residue-specific interactions in the unfolded state remain elusive. Here we introduce a method derived from the Wyman-Tanford theory to determine residue-specific pK(a)'s in the unfolded state.

Predicting pKa values with continuous constant pH molecular dynamics.

Knowledge of pK(a) values is important for understanding structure and function relationships in proteins. Over the past two decades, theoretical methods for pK(a) calculations have been mainly based on macroscopic models, in which the protein is considered as a low-dielectric cavity embedded in a high-dielectric continuum. In recent years, constant pH molecular dynamics methods have been developed based on a microscopic description of the protein.