Michael J. Potter

The Physical Basis of Nucleic Acid Base Stacking in Water

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.

Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms

A fast, accurate method of assigning partial atomic charges is described. The method is based upon the concept of electronegativity equalization and is parametrized to fit electrostatic potentials obtained from ab initio quantum calculations. A novel algorithm for identifying alternate resonance forms is used to ensure that chemically equivalent atoms are assigned equal charges. The resulting charges are independent of conformation, yield good agreement with ab initio electrostatic potentials, and are similar to standard force field charges for common biochemical components. The method is broadly parametrized and generates charges for a drug-like compound in about 0.45 s on a 2.26 GHz Pentium 4 PC. It should thus be useful in a range of applications, such as molecular design and QSAR. The resonance algorithm is expected to have additional applications, such as in atom-typing and detection of molecular symmetry.

Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes

Accurate free-energy calculations provide mechanistic insights into molecular recognition and conformational equilibrium. In this work, we performed free-energy calculations to study the thermodynamic properties of different states of molecular systems in their equilibrium basin, and obtained accurate absolute binding free-energy calculations for protein-ligand binding using a newly developed M2 algorithm. We used a range of Asp-Phe-Gly (DFG)-in/out p38α mitogen-activated protein kinase inhibitors as our test cases. We also focused on the flexible DFG motif, which is closely connected to kinase activation and inhibitor binding. Our calculations explain the coexistence of DFG-in and DFG-out states of the loop and reveal different components (e.g., configurational entropy and enthalpy) that stabilize the apo p38α conformations. To study novel ligand-binding modes and the key driving forces behind them, we computed the absolute binding free energies of 30 p38α inhibitors, including analogs with unavailable experimental structures. The calculations revealed multiple stable, complex conformations and changes in p38α and inhibitor conformations, as well as balance in several energetic terms and configurational entropy loss. The results provide relevant physics that can aid in designing inhibitors and understanding protein conformational equilibrium. Our approach is fast for use with proteins that contain flexible regions for structure-based drug design.

Biomarkers of chemotaxis and inflammation in cerebrospinal fluid and serum in individuals with HIV-1 subtype C versus B

A defective chemokine motif in the HIV-1 Tat protein has been hypothesized to alter central nervous system cellular trafficking and inflammation, rendering HIV-1 subtype C less neuropathogenic than B. To evaluate this hypothesis, we compared biomarkers of cellular chemotaxis and inflammation in cerebrospinal fluid (CSF) and serum in individuals infected with HIV-1 subtypes B (nu2009=u200927) and C (nu2009=u200925) from Curitiba, Brazil. None had opportunistic infections. Chemokines (MCP-1, MIP-1α, MIP-1β, RANTES, IP-10) and cytokines (TNF-α, IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-7, IL-10) were measured using the multiplex bead suspension array immunoassays or ELISA HD. CSF and serum biomarker concentrations were compared between subtype B and C groups and HIV-positive and HIV-negative subjects (Nu2009=u200919) using an independent group t test (unadjusted analysis) and linear regression (adjusted analysis), controlling for nadir CD4 and CSF and plasma HIV RNA suppression. CSF levels of cytokines and chemokines were significantly (pu2009<u20090.05) elevated in HIV-positive versus HIV-negative participants for 7/13 biomarkers measured, but levels did not differ for subtypes B and C. Serum levels were significantly elevated for 4/13 markers, with no significant differences between subtypes B and C. Although pleocytosis was much more frequent in HIV-positive than in HIV-negative individuals (27 vs. 0xa0%), subtypes B and C did not differ (32 and 22xa0%; pu2009=u20090.23). We did not find molecular evidence to support the hypothesis that intrathecal chemotaxis and inflammation is less in HIV-1 subtype C than in subtype B. Biomarker changes in CSF were more robust than in serum, suggesting compartmentalization of the immunological response to HIV.

Application of Poisson—Boltzmann solvation forces to macromolecular simulations

One of the most difficult problems encountered in the dynamical simulation of large macromolecular systems is how to deal adequately with the huge number of atomic interactions involved. For aqueous-phase simulations the computational burden associated with solvent water molecules can easily outstrip that associated with the macromolecule, even though the behavior of the solvent itself may not be of much interest. Not surprisingly therefore, considerable interest has been focused on the use of methods in which explicit solvent water molecules are replaced by an implicit dielectric continuum representation; an excellent review of such methods was given by Sharp [1] in the previous volume of this series. Perhaps the most generally accepted continuum-based approach centers on the use of the Poisson—Boltzmann (PB) equation of classical electrostatics [2], a method which owes its success to the fact that many solvation-related phenomena (with the notable exception of the hydrophobic effect) appear to be essentially electrostatic in nature. Until very recently, use of the PB approach has largely been restricted to calculations involving static representations of molecular structure, but the recent development of methods to obtain solvation forces from the PB equation [3] means that it can now, in principle, also be used in dynamics simulations. Applications of the former type have been comprehensively reviewed in the literature [2] and are not discussed further in this article; instead, we restrict our attention to the potential use of PB electrostatics in dynamical simulations of macromolecules.

Blood-CSF barrier and compartmentalization of CNS cellular immune response in HIV infection.

HIV infection is persistent in the CNS, to evaluate the compartmentalization of the CNS immune response to HIV, we compared soluble markers of cellular immunity in the blood and CSF among HIV- (n=19) and HIV+ (n=68), as well as among HIV participants with or without CSF pleocytosis. Dysfunction of the blood cerebrospinal fluid barrier (BCSFB) was common in HIV participants. CSF levels of TNFα, IFNγ, IL-2, IL-6, IL-7, IL-10, IP-10, MIP-1α, MIP-1β, and RANTES were significantly higher in participants with CSF pleocytosis (P<0.05); serum levels of these biomarkers were comparable. The CNS immune response is compartmentalized, and remains so despite the BCSFB dysfunction during HIV infection; it is markedly reduced by virology suppression, although BCSFB dysfunction persists on this subgroup.

MOLECULAR DYNAMICS OF CRYPTOPHANE AND ITS COMPLEXES WITH TETRAMETHYLAMMONIUM AND NEOPENTANE USING A CONTINUUM SOLVENT MODEL

Time scales currently obtainable in explicit–solvent molecular dynamics simulations are inadequate for the study of many biologically important processes. This has led to increased interest in the use of continuum solvent models. For such models to be used effectively, it is important that their behavior relative to explicit simulation be clearly understood. Accordingly, 5 ns stochastic dynamics simulations of a derivative of cryptophane‐E alone, and complexed with tetramethylammonium and neopentane were carried out. Solvation electrostatics were accounted for via solutions to the Poisson equation. Nonelectrostatic aspects of solvation were incorporated using a surface area‐dependent energy term. Comparison of the trajectories to those from previously reported 25 ns explicit–solvent simulations shows that use of a continuum solvent model results in enhanced sampling. Use of the continuum solvent model also results in a considerable increase in computational efficiency. The continuum solvent model is found to predict qualitative structural characteristics that are similar to those observed in explicit solvent. However, some differences are significant, and optimization of the continuum parameterization will be required for this method to become an efficient alternative to explicit–solvent simulation.u2003©1999 John Wiley & Sons, Inc.u2003J Comput Chem 20: 956–970, 1999

Modeling Molecular Recognition: Theory and Application

Abstract Efficient, reliable methods for calculating the binding affinities of noncovalent complexes would allow advances in a variety of areas such as drug discovery and separation science. We have recently described a method that accommodates significant physical detail while remaining fast enough for use in molecular design. This approach uses the predominant states method to compute free energies, an empirical force field, and an implicit solvation model based upon continuum electrostatics. We review applications of this method to systems ranging from small molecules to protein-ligand complexes.

Biomarkers of neuronal injury and amyloid metabolism in the cerebrospinal fluid of patients infected with HIV-1 subtypes B and C

Based on prior reports that the HIV-1 Tat protein modulates amyloid-beta (Aβ) metabolism, this study aimed to compare CSF neural injury biomarkers between 27 patients with HIV subtype B, 26 patients with HIV subtype C, 18 healthy HIV-negative controls, and 24 patients with Alzheimer’s disease (AD). Immunoassays were used to measure soluble amyloid precursor protein α and β (sAPPα, sAPPβ), Aβ oligomers 38, 40, 42, and Aβ-total; phosphorylated tau (P-tau181), and total tau (T-tau). Comparisons between HIV(+) and HIV(−) (including AD) were adjusted by linear regression for gender and age; HIV subtype comparisons were adjusted for nadir CD4 and plasma viral load suppression. The p values were corrected for multiple testing with the Benjamini-Hochberg procedure. CSF Aβ-42 and Hulstaert (P-tau181) index were lower in HIV1-C than B (pxa0=xa00.03, and 0.049 respectively); subtypes did not differ on other CSF biomarkers or ratios. Compared to AD, HIV(+) had lower CSF levels of T-tau, P-tau181 (pxa0<xa00.001), and sAPPα (pxa0=xa00.041); HIV(+) had higher CSF Aβ-42 (pxa0=xa00.002) and higher CSF indexes: [Aß-42/(240xa0+xa01.18xa0T-tau)], P-tau181/Aβ-42, T-tau/Aβ-42, P-tau181/T-tau, sAPPα/β (all pxa0≤xa00.01) than AD. Compared to HIV(−), HIV(+) had lower CSF Aβ-42, and T-tau (all pxa0≤xa00.004). As conclusion, amyloid metabolism was influenced by HIV infection in a subtype-dependent manner. Aß-42 levels were lower in HIV1-C than B, suggesting that there may be greater deposition of Aß-42 in HIV1-C. These findings are supported by CSF Hulstaert (P-tau181) index. Differences between HIV and AD in the patterns of Aß and Tau biomarkers suggest that CNS HIV infection and AD may not share some of same mechanisms of neuronal injury.

HIV, prospective memory, and cerebrospinal fluid concentrations of quinolinic acid and phosphorylated Tau

There is mounting evidence that prospective memory (PM) is impaired during HIV infection despite treatment. In this prospective study, 66 adults (43 HIV+ and 23 HIV negative) underwent PM assessment and cerebrospinal fluid (CSF) examination. HIV+ participants had significantly lower PM but significantly higher CSF concentrations of CXCL10 and quinolinic acid (QUIN). Higher CSF phosphorylated Tau (pTau) was associated with worse PM. In a secondary analysis excluding outliers, higher QUIN correlated with higher pTau. CSF QUIN is thus elevated during HIV infection despite antiretroviral therapy and could indirectly contribute to impaired PM by influencing the formation of pTau.