We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments.

Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated. molecular machines | elastic-network models | conformational relaxation | mechanochemical motions | nonequilibrium dynamics P rotein machines and, particularly, molecular motors are of fundamental importance for biological cells. Underlying their organized activity are ordered conformational motions driven in proteins by ATP hydrolysis (1). Such cyclic motions are on the scales of milliseconds and thus are too slow to be followed in molecular dynamics (MD) simulations. On the other hand, simple physical modeling in terms of stochastic automata, oscillators, or Brownian ratchets lacks conformational aspects of protein dynamics (2-4). Coarse-grained models of molecular motors, which allow structurally resolved dynamical simulations of entire operation cycles, are therefore needed.In the last decade, coarse-grained descriptions of proteins, based on elastic-network models (ENM), have been proposed and investigated (5-9). In such models, each residue is usually considered as a single particle. The particles interact via elastic potentials, introduced in such a way that the minimum of elastic energy for a network is reached for a configuration coinciding with the known equilibrium conformation of the considered protein. Despite their high simplicity, ENM are able to correctly predict conformational changes induced by ligand binding. Such network models have also been used to describe conformational relaxation (10, 11) and functional mechanochemical motions in motor proteins (10, 12). Moreover, coarse-grained descriptions of DNA molecules, modeling them as semiflexible elastic polymers, are broadly used (13-15). Here, we show that entire operation cycles of a protein motor, involving its interactions with DNA, can be computationally traced by combining the elastic-network relaxation description for a protein with the elastic polymer description for DNA.Hepatitis C virus (HCV) helicase is a motor protein that, translocating itself, unwinds duplex RNA or DNA (see review in ref. 16). Experimental and theoretical investigations of this motor, representative for a broad class of helicases (17), have been performed (18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Experimental data suggest that ratcheting inchworm translocation (19,27,28) and spring-loaded DNA unwinding (26) constitute the principal mechanism of its operation. The elasticnetwork description for HCV ...

Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects and functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting of the in silico design of synthetic structures, which, as the principal element of allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling. In the designed structures, allosteric interactions were analyzed in terms of strain propagation, and simple pathways that emerged during evolution were identified as signatures through which long-range communication was established. Moreover, robustness of allosteric performance with respect to mutations was demonstrated. As it turned out, the designed prototype structures reveal dynamical properties resembling those found in real allosteric proteins. Hence, they may serve as toy models of complex allosteric systems, such as proteins. Application of the developed modeling scheme to the allosteric transition in the myosin V molecular motor was also demonstrated.

While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.