Molecular Surface Maps

We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surface Map concisely shows arbitrary attributes of the original molecular surface, such as biochemical properties or geometrical features. This results in an intuitive overview, which allows researchers to assess all molecular surface attributes at a glance. Our representation can be used as a visual summarization of a molecule's interface with its environment. In particular, Molecular Surface Maps simplify the analysis and comparison of different data sets or points in time. Furthermore, the map representation can be used in a Space-time Cube to analyze time-dependent data from molecular simulations without the need for animation. We show the feasibility of Molecular Surface Maps for different typical analysis tasks of biomolecular data.

Binding of Solvent Molecules to a Protein Surface in Binary Mixtures Follows a Competitive Langmuir Model

The binding of solvent molecules to a protein surface was modeled by molecular dynamics simulations of of Candida antarctica (C. antarctica) lipase B in binary mixtures of water, methanol, and toluene. Two models were analyzed: a competitive Langmuir model which assumes identical solvent binding sites with a different affinity toward water (KWat), methanol (KMet), and toluene (KTol) and a competitive Langmuir model with an additional interaction between free water and already bound water (KWatWat). The numbers of protein-bound molecules of both components of a binary mixture were determined for different compositions as a function of their thermodynamic activities in the bulk phase, and the binding constants were simultaneously fitted to the six binding curves (two components of three different mixtures). For both Langmuir models, the values of KWat, KMet, and KTol were highly correlated. The highest binding affinity was found for methanol, which was almost 4-fold higher than the binding affinities of water and toluene (KMet ≫ KWat ≈ KTol). Binding of water was dominated by the water-water interaction (KWatWat). Even for the three protein surface patches of highest water affinity, the binding affinity of methanol was 2-fold higher than water and 8-fold higher than toluene (KMet > KWat > KTol). The Langmuir model provides insights into the protein destabilizing mechanism of methanol which has a high binding affinity toward the protein surface. Thus, destabilizing solvents compete with intraprotein interactions and disrupt the tertiary structure. In contrast, benign solvents such as water or toluene have a low affinity toward the protein surface. Water is a special solvent: only few water molecules bind directly to the protein; most water molecules bind to already bound water molecules thus forming water patches. A quantitative mechanistic model of protein-solvent interactions that includes competition and miscibility of the components contributes a robust basis for solvent and protein engineering.

Molecular mechanism of deactivation of C. antarctica lipase B by methanol

The catalytic activity of Candida antarctica lipase B upon alcoholysis of a constant concentration of 15.2% vinyl acetate (vol/vol) and varying concentrations of methanol (0.7-60%) in toluene was determined experimentally by measuring the initial reaction velocity. The molecular mechanism of the deactivation of the enzyme by methanol was investigated by fitting the experimental data to a kinetic model and by molecular dynamics simulations of C. antarctica lipase B in toluene-methanol-water mixtures. The highest catalytic activity (280 U/mg) was observed at methanol concentrations as low as 0.7% methanol (vol/vol), followed by a sharp decrease at higher methanol concentrations. For methanol concentrations above 10% (vol/vol), catalytic activity was at 30% of the maximum activity. A variation of water activity in the range 0.02-0.09 had only minor effects. These experimental observations are described by a simple kinetic model using three assumptions: (1) a ping-pong bi-bi mechanism of the enzyme, (2) competitive inhibition by the substrate methanol, and (3) by describing enzyme kinetics by the thermodynamic activities of the substrates rather than by their concentrations. Two equilibrium constants of methanol (KM,MeOH=0.05 and Ki,MeOH=0.23) were derived by modeling methanol binding to the substrate binding site of the lipase in molecular dynamics simulations of protein-solvent systems at atomic resolution. Thus, the sharp maximum of catalytic activity of C. antarctica lipase B at 0.7% methanol is a direct consequence of the fact that methanol-toluene mixtures are far from ideal. Understanding the thermodynamics of solvent mixtures is prerequisite to a quantitative model of enzymatic activity in organic solvents.