Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch.

Riboswitches are messenger RNA (mRNA) fragments binding specific small molecules to regulate gene expression. A synthetic N1 riboswitch, inserted into yeast mRNA controls the translation of a reporter gene in response to neomycin. However, its regulatory activity is sensitive to single-point RNA mutations, even those distant from the neomycin binding site.

Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics.

Molecular dynamics (MD) simulations are increasingly used to study various biological processes such as protein folding, conformational changes, and ligand binding. These processes generally involve slow dynamics that occur on the millisecond or longer timescale, which are difficult to simulate by conventional atomistic MD. Recently, we applied a two-dimensional (2D) replica-exchange MD (REMD) method, which combines the generalized replica exchange with solute tempering (gREST) with the replica-exchange umbrella sampling (REUS) in kinase-inhibitor binding simulations, and successfully observed multiple ligand binding/unbinding events.

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins.

Large-scale conformational transitions in multi-domain proteins are often essential for their functions. To investigate the transitions, it is necessary to explore multiple potential pathways, which involve different intermediate structures. Here, we present a multi-basin (MB) coarse-grained (CG) structure-based Go̅ model for describing transitions in proteins with more than two moving domains.

Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.

Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBP) in solution.

Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio.

The dual-basin Gō-model is a structural-based coarsegrained model for simulating a conformational transition between two known structures of a protein. Two parameters are required to produce a dual-basin potential mixed using two single-basin potentials, although the determination of mixing parameters is usually not straightforward. Here, we have developed an efficient scheme to determine the mixing parameters using the Multistate Bennett Acceptance Ratio (MBAR) method after short simulations with a set of parameters.

evERdock BAI: Machine-learning-guided selection of protein-protein complex structure.

Computational techniques for accurate and efficient prediction of protein-protein complex structures are widely used for elucidating protein-protein interactions, which play important roles in biological systems. Recently, it has been reported that selecting a structure similar to the native structure among generated structure candidates (decoys) is possible by calculating binding free energies of the decoys based on all-atom molecular dynamics (MD) simulations with explicit solvent and the solution theory in the energy representation, which is called evERdock. A recent version of evERdock achieves a higher-accuracy decoy selection by introducing MD relaxation and multiple MD simulations/energy calculations; however, huge computational cost is required.

Essential ion binding residues for Na flow in stator complex of the Vibrio flagellar motor.

The bacterial flagellar motor is a unique supramolecular complex which converts ion flow into rotational force. Many biological devices mainly use two types of ions, proton and sodium ion. This is probably because of the fact that life originated in seawater, which is rich in protons and sodium ions.

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations.

A method for evaluating binding free energy differences of protein-protein complex structures generated by protein docking was recently developed by some of us. The method, termed evERdock, combined short (2 ns) molecular dynamics (MD) simulations in explicit water and solution theory in the energy representation (ER) and succeeded in selecting the near-native complex structures from a set of decoys. In the current work, we performed longer (up to 100 ns) MD simulations before employing ER analysis in order to further refine the structures of the decoy set with improved binding free energies.

Proton Wire Dynamics in the Green Fluorescent Protein.

Inside proteins, protons move on proton wires (PWs). Starting from the highest resolution X-ray structure available, we conduct a 306 ns molecular dynamics simulation of the (A-state) wild-type (wt) green fluorescent protein (GFP) to study how its PWs change with time. We find that the PW from the chromophore via Ser205 to Glu222, observed in all X-ray structures, undergoes rapid water molecule insertion between Ser205 and Glu222.

The hole in the barrel: water exchange at the GFP chromophore.

Internal water molecules in proteins are conceivably part of the protein structure, not exchanging easily with the bulk. We present a detailed molecular dynamics study of the water molecule bound to the green fluorescent protein (GFP) chromophore that conducts its proton following photoexcitation. It readily exchanges above 310 K through a hole that forms between strands 7 and 10, due to fluctuations in the 6-7 loop.

Visualizing proton antenna in a high-resolution green fluorescent protein structure.

"Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.

Mapping proton wires in proteins: carbonic anhydrase and GFP chromophore biosynthesis.

We have developed an algorithm for mapping proton wires in proteins and applied it to the X-ray structures of human carbonic anhydrase II (CA-II), the green fluorescent protein (GFP), and some of their mutants. For both proteins, we find more extensive proton wires than typically reported. In CA-II the active site wire exits to the protein surface, and leads to Glu69 and Asp72, located on an electronegative patch on the rim of the active site cavity.