Molecular dynamics simulation with a continuum electrostatic model of the solvent

The accuracy and simplicity of the Poisson-Boltzmann electrostatics model has led to the suggestion that it might offer an efficient solvent model for use in molecular mechanics calculations on biomolecules. We report a successful merger of the Poisson-Boltzmann and molecular dynamics approaches, with illustrative calculations on the small solutes dichloroethane and alanine dipeptide. The algorithm is implemented within the program UHBD. Computational efficiency is achieved by the use of rather coarse finite difference grids to solve the Poisson-Boltzmann equation. Nonetheless, the conformational distributions generated by the new method agree well with reference distributions obtained as Boltzmann distributions from energies computed with fine finite difference grids. The conformational distributions also agree well with the results of experimental measurements and conformational analyses using more detailed solvent models. We project that when multigrid methods are used to solve the finite difference problem and the algorithm is implemented on a vector supercomputer, the computation of solvent electrostatic forces for a protein of modest size will add only about 0.1 s computer time per simulation step relative to a vacuum calculation. © 1995 by John Wiley & Sons, Inc.     

Combination of two-dimensional gel electrophoresis with microsequencing and amino acid composition analysis: improvement of speed and sensitivity in protein characterization

High-resolution two-dimensional polyacrylamide electrophoresis (2-DE) is commonly used as an analytical approach to resolve and detect most of the numerous protein species of an organism. However, the isolation of microgram amounts of protein in a 2-DE spot in a form suitable for microsequence analysis and amino acid composition analysis is a key step in the chemical characterization of these proteins. With the development of chemically inert membranes it is now possible to retain proteins present in low quantities from the polyacrylamide matrix with high yields. The immobilized proteins are suitable for direct sequence analysis and amino acid composition analysis. The combination of protein chemical and electrophoretic techniques makes it possible to obtain chemical information from subpicomole quantities of protein, resulting in the availability of a new set of biologically important proteins for structural analysis. This paper summarizes the methods and strategies for the chemical protein analysis of 2-DE spots in our laboratory.     

Quantitative analysis of immobilized proteins and protein mixtures by amino acid analysis

Biomolecular surface engineering of materials often requires precise, versatile and efficient quantification of immobilized proteins at solid surfaces. Acidic hydrolysis of surface-bound proteins and subsequent HPLC analysis of fluorescence-derivatized amino acids were adapted and critically evaluated for that purpose. Contaminations and concentration-dependent amino acid retrieval during HPLC were found to influence the accuracy of the method. In addition to the choice of adequate conditions for hydrolysis, derivatization and chromatographic separation extensions of the data evaluation were suggested to improve the accuracy of the approach when applied to single protein systems: comparing the experimentally obtained amino acid ratio to the protein constitution enabled to identify the properly separated and detected amino acids. Those amino acids were selected for a more precise calculation of the amount of immobilized protein. To further increase the accuracy of the method, the retrieval of amino acids corresponding to protein amounts in the range between 0.5 and 4.0 microg was analyzed for a variety of proteins of interest to derive protein-specific correction factors. The evaluation of amino acid data was furthermore applied to quantify binary protein mixtures at similar settings. This method was proven useful to detect the composition of protein mixtures throughout a wide range of absolute and relative concentrations.     

High sensitivity analysis of phenylthiohydantoin amino acid derivatives by electrospray mass spectrometry

A new methodology has been developed for high sensitivity electrospray ionization mass spectrometric analyses of phenylthiohydantoin (PTH) amino acid derivatives. Key components of the methodology are the use of a solvent system consisting of methanol/dichloromethane (1:1 v/v) containing 5-mM lithium triflate, a stainless steel electrode having a relatively large surface area, and a microscale electrospray nozzle that provides for stable electrospray at flow rates in the range of 100–500 nL/min. A linear response for the absolute signal intensity of the protonated molecule was observed for a number of derivatives over the concentration range of 50–1000 fmol/µL. For all except the arginine derivative, there was a decrease in the signal intensity with increasing flow rate with 100–300 nL/min being optimum. Collision induced dissociation (CID) product ion spectra were obtained for 21 derivatives including carboxymethyl cysteine and dehydrothreonine. Leucine and isoleucine can be distinquished on the basis of their CID product ion spectra. A subfemtomole detection limit was demonstrated for the phenylalanine PTH derivative in a selected reaction monitoring (SRM) experiment. Samples from an automated Edman microsequencer run have been analyzed using the new technique and compared to results obtained by conventional high-performance liquid chromatography analysis with UV detection. This work demonstrates the feasibility of using mass spectrometry to identify and quantitate the products generated by automated protein microsequencing using standard Edman degradation chemistry.     

Calculation of electrostatic and polarization energies from electron densities

We investigate procedures for calculating the electrostatic and polarization energies, Ees and Epol, associated with noncovalent interactions. The starting points are the electron densities of the isolated components and the complex; these could be obtained either computationally or experimentally. A slightly modified version of a scheme proposed by Gavezzotti is used to carry out numerical integrations over these electron densities. Our approach to estimating Epol is based upon partitioning the charge distributions of the components into overlapping and nonoverlapping regions. The effects of varying the integration parameters, computational techniques and basis sets are examined in detail for several noncovalently bound molecular dimers. Our results are in good agreement with the values of Ees and Epol produced by other methods, which require analytical integrations over interaction Hamiltonian matrix elements.     

Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework

Electrostatic interactions between biological molecules are crucially influenced by their aqueous environment, with efficient and accurate models of solvent effects required for robust molecular design strategies. Continuum electrostatic models provide a reasonable balance between computational efficiency and accurate system representation. In this article, I review two specific molecular design strategies, charge optimization and combinatorial design, paying particular attention to how the continuum framework (also briefly described herein) successfully enables both theoretical insights and molecular designs and presents a challenge in design applications due to what I call “the isostericity constraint.” Efforts to work around the isostericity constraint and other challenges are discussed. Additionally, particular emphasis is placed on using such models in the rational design of particularly tight, specific, or promiscuous interactions, in keeping with the increased sophistication of current molecular design applications.     

Advances in amino acid analysis

Amino acids are important targets for metabolic profiling. For decades, amino acid analysis has been accomplished by either cation-exchange or reversed-phase liquid chromatography coupled to UV absorbance or fluorescence detection of pre-column or post-column-derivatized amino acids. Recent years have seen great progress in the development of direct-infusion or hyphenated mass spectrometry in the analysis of free amino acids in physiological fluids, because mass spectrometry not only matches optical detection in sensitivity, but also offers superior selectivity. The advent of cryo-probes has also brought NMR spectroscopy within the detection limits required for the analysis of free amino acids. But there is still room for further improvement, including expansion of the analyte spectrum, reduction of sample preparation and analysis time, automation, and synthesis of affordable isotope standards. Figure Fully automated gas chromatography-mass spectrometry analysis of amino acids.     

Microfluidics in amino acid analysis

Microfluidic devices have been widely used to derivatize, separate, and detect amino acids employing many different strategies. Virtually zero-dead volume interconnections and fast mass transfer in small volume microchannels enable dramatic increases in on-chip derivatization reaction speed, while only minute amounts of sample and reagent are needed. Due to short channel path, fast subsecond separations can be carried out. With sophisticated miniaturized detectors, the whole analytical process can be integrated on one platform. This article reviews developments of lab-on-chip technology in amino acid analysis, it shows important design features such as sample preconcentration, precolumn and postcolumn amino acid derivatization, and unlabeled and labeled amino acid detection with focus on advanced designs. The review also describes important biomedical and space exploration applications of amino acid analysis on microfluidic devices.     

A statistical model for predicting protein folding rates from amino acid sequence with structural class information

Prediction of protein folding rates from amino acid sequences is one of the most important challenges in molecular biology. In this work, I have related the protein folding rates with physical-chemical, energetic and conformational properties of amino acid residues. I found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and folding rates of two- and three-state proteins, indicating the importance of native state topology in determining the protein folding rates. I have formulated a simple linear regression model for predicting the protein folding rates from amino acid sequences along with structural class information and obtained an excellent agreement between predicted and experimentally observed folding rates of proteins; the correlation coefficients are 0.99, 0.96 and 0.95, respectively, for all-alpha, all-beta and mixed class proteins. This is the first available method, which is capable of predicting the protein folding rates just from the amino acid sequence with the aid of generic amino acid properties and structural class information.     

Chromatographic amino acid analysis of protein hydrolysed in polyacrylamide after removal of ammonia

Summary A simple method for the removal of NH₃ from amino acids is presented. The method is based on a cation-exchange resin from which amino acids are eluted with NH₄OH. The eluent is then removed under reduced pressure. The method allows the ninhydrin-based detection of amino acids after hydrolysis of stained protein bands in polyacrylamide gels. This was previously not possible since NH₃ produced by the hydrolysis of polyacrylamide interferes with the ninhydrin-detection of basic amino acids. The method should also be applicable to the detection of amino acids with o-phthalaldehyde.     

Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model

In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson–Boltzmann/solvent‐accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self‐consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well‐experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0.8 kcal/mol versus 2.5 kcal/mol for the CHARMM36 additive force field. The polarization work associated with the solute transfer from the gas‐phase to the polar solvent, a term neglected in the framework of additive force fields, was found to make a large contribution to the total solvation free energy, comparable to the polar solute–solvent solvation contribution. The Drude PB/SASA also reproduces well the electronic polarization from the explicit solvent simulations of a small protein, BPTI. Model validation was based on comparisons with the experimental relative binding free energies of 371 single alanine mutations. With the Drude PB/SASA model the root mean square deviation between the predicted and experimental relative binding free energies is 3.35 kcal/mol, lower than 5.11 kcal/mol computed with the CHARMM36 additive force field. Overall, the results indicate that the main limitation of the Drude PB/SASA model is the inability of the SASA term to accurately capture non‐polar solvation effects. © 2018 Wiley Periodicals, Inc.     

Towards lignin-protein crosslinking: amino acid adducts of a lignin model quinone methide

The polyaromatic structure of lignin has long been recognized as a key contributor to the rigidity of plant vascular tissues. Although lignin structure was once conceptualized as a highly networked, heterogeneous, high molecular weight polymer, recent studies have suggested a very different configuration may exist in planta. These findings, coupled with the increasing attention and interest in efficiently utilizing lignocellulosic materials for green materials and energy applications, have renewed interest in lignin chemistry. Here we focus on quinone methides (QMs)—key intermediates in lignin polymerization—that are quenched via reaction with cell-wall-available nucleophiles. Reactions with alcohol and uronic acid groups of hemicelluloses, for example, can lead to lignin-carbohydrate crosslinks. Our work is a first step toward exploring potential QM reactions with nucleophilic groups in cell wall proteins. We conducted a model compound study wherein the lignin model compound guaiacylglycerol-β-guaiacyl ether 1, was converted to its QM 2, then reacted with amino acids bearing nucleophilic side-groups. Yields for the QM-amino acid adducts ranged from quantitative in the case of QM-lysine 3, to zero (no reaction) in the cases of QM-threonine (Thr) 10 and QM-hydroxyproline (Hyp) 11. The structures of the QM-amino acid adducts were confirmed via 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) calculations, thereby extending the lignin NMR database to include amino acid crosslinks. Some of the QM-amino acid adducts formed both syn- and anti-isomers, whereas others favored only one isomer. Because the QM-Thr 10 and QM-Hyp 11 compounds could not be experimentally prepared under conditions described here but could potentially form in vivo, we used DFT to calculate their NMR shifts. Characterization of these model adducts extends the lignin NMR database to aid in the identification of lignin-protein linkages in more complex in vitro and in vivo systems, and may allow for the identification of such linkages in planta.     

Nonnatural amino acid ligands in heme protein design

The de novo design, synthesis, and characterization of a four-alpha-helix bundle scaffold containing heme ligated by 4-beta-(pyridyl)-l-alanine (Pal) is presented. The protein scaffold is highly helical, stable, and conformationally specific in the apo-state. Incorporation of heme using the designed bis-Pal axial ligation is shown using UV-visible and EPR spectroscopies. The observed heme midpoint reduction potential, +58 mV versus SHE, is 287 mV (6.8 kcal/mol) higher than the analogous bis-histidine-ligated heme protein.     

Theory of electron solvation in polar liquids: a continuum model

The solvation of electrons in polar liquids is analyzed on the basis of an extended continuum model. In addition to the long-range electron-dipole interaction two short-range interactions are introduced. Among others one accounts for interactions with groups capable of forming hydrogen bonds and the second for quadrupolar characteristics of the liquid molecules. Both are induced by the orientation of the molecular dipole. Applying the scaling method a proper reaction coordinate is introduced and the solvation dynamics are discussed for the electron in the electronic ground state and after excitation to the p-type excited state. The observed spectral evolution of the transient absorption spectra, after two photon excitations for electrons in water and in methanol, is well described by this theory. An analytic estimate for the nonradiative deactivation from the electronically excited solvated electron is found to be consistent with an observed lifetime of 50 fs for the electron in water. The theory predicts an about three times slower internal conversion in methanol as solvent in comparison with water.