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A new approach to comparative modeling of proteins, TRACER, is described and benchmarked against classical modeling procedures. The new method unifies true three-dimensional threading with coarse-grained sampling of query protein conformational space. The initial sequence alignment of a query protein with a template is not required, although a template needs to be somehow identified. The template is used as a multi-featured fuzzy three-dimensional scaffold. The conformational search for the query protein is guided by intrinsic force field of the coarse-grained modeling engine CABS and by compatibility with the template scaffold. During Replica Exchange Monte Carlo simulations the model chain representing the query protein finds the best possible structural alignment with the template chain, that also optimizes the intra-protein interactions as approximated by the knowledge based force field of CABS. The benchmark done for a representative set of query/template pairs of various degrees of sequence similarity showed that the new method allows meaningful comparative modeling also for the region of marginal, or non-existing, sequence similarity. Thus, the new approach significantly extends the applicability of comparative modeling.
Protein modeling could be done on various levels of structural details, from simpli­fied lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular me­chanics. Here I describe a new high resolution reduced model, its force field and ap­plications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sam­pling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic pro­tein-like conformational biases, statistical potentials for the short-range confor- mational propensities, a model of the main chain hydrogen bonds and context-de­pendent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.
Ripple phase modelling was achievable by taking into consideration the dipole structure of the polar heads of model membrane molecules. Computer simulations enabled the selective analysis of a model membrane. Considering only the hydrophobic part of the lipid membrane, the gel-fluid transition stage can be obtained in such a simulation. Assuming an additional degree of freedom, the entire molecule can move along the normal to the membrane surface projected from two C-C bonds. The amounts of shifted lipids were 17% and 33% at temperatures of 300 K (gel) and 330 K (fluid), respectively. Taking into account only polar head interactions in media of different ionic strength I, dielectric constant ε, and an effective charge and temperature, we could observe the same behaviour of the examined system independently of the values of I and ε when the charge was reduced to q/2. The amount of shifted heads at 300 K decreases sharply with the reduced charge value, with an accompanying increase in the number of “standing” polar heads. Summing up, it can be stated that hydrocarbon lipid chains exhibit a greater tendency to displacement in the fluid state than in the gel state. However, the polar heads behave in the opposite way: there are more displaced heads at 300 K than at 330 K. Thus, the overall analysis of the interactions between the molecules of the model membrane should enable us to find model parameters suitable for studying the lipid membrane at a wide range of temperatures. Finally, an electrostatic profile close to the membrane surface could be estimated in different membrane states. This should be useful in membrane-biologically active compound interaction analysis.
A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.
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