A. Popinako

Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity

Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core).

Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation

The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF. We identified the specific amino acid residues in GMF and Arp2/3 complex that stabilize the interactions and estimated the mean force profile for the GMF using umbrella sampling. Phylogenetic and structural analyses of the recently defined GMF binding site on the Arp3 subunit indicate a new mechanism for Arp2/3 complex inactivation that involves interactions between the Arp2/3 complex and GMF at two binding sites.

Analysis of the Interactions between Arp2/3 Complex and an Inhibitor Arpin by Molecular Dynamics Simulation

The Arp2/3 complex is one of the main regulators of the actin cytoskeleton and a basic molecular machine that nucleates the branched actin filaments. In this work, we studied the interaction of the Arp2/3 complex with its inhibitor, arpin, and revealed the amino-acid residues that are responsible for complex formation. The free-energy calculation for arpin binding to the Arp2/3 complex was performed using umbrella sampling. It has been shown that the dissociation constant of the Arp2/3–arpin complex is higher on average than that of Arp2/3 complexes with other inhibitors. Two arpin binding sites with different affinities were identified on the surface of the Arp2/3 complex. The mechanism of the inhibition of the Arp2/3 complex by arpin is discussed.

Structural adaptation of active center channels of octaheme nitrite reductases from the haloalkaliphilic bacteria Thioalkalivibrio nitratireducens to a proton deficit

Study of the adaptation mechanisms of proteins from extremophiles paves the way for the development of new biocatalysts that are resistant to extreme conditions. Here, we studied the structural adaptation of active center channels of octaheme nitrite reductase from the haloalkophilic bacterium Thioalkalivibrio nitratireducens (TvNiR) to high pH. Comparative analysis of the structures of octaheme nitrite reductases adapted to different environmental conditions revealed unique adaptation mechanisms for TvNiR, which play an important role in binding rare protons and substrate and product migration in the active-site channels.

Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues

The study of structural adaptations of proteins from polyextremophilic organisms using computational molecular dynamics method is appealing because the obtained knowledge can be applied to construction of synthetic proteins with high activity and stability in polyextreme media which is useful for many industrial applications. To investigate molecular adaptations to high temperature, we have focused on a superthermostable short-chain dehydrogenase TsAdh319 from the Thermococcus sibiricus polyextremophilic archaeon and its closest structural homologues. Molecular dynamics method is widely used for molecular structure refinement, investigation of biological macromolecules motion, and, consequently, for interpreting the results of certain biophysical experiments. We performed molecular dynamics simulations of the proteins at different temperatures. Comparison of root mean square fluctuations (RMSF) of the atoms in thermophilic alcohol dehydrogenases (ADHs) at 300 K and 358 K revealed the existence of stable r...

Numerical Modelling of Ion Transport in 5-HT3 Serotonin Receptor Using Molecular Dynamics

Cation selective ligand-gated ion channels are pore-forming membrane proteins. They are responsible for generating of transmembrane voltage and action potential, playing an important role in functioning of nervous systems. Mathematical modelling of transmembrane transport in membrane and membrane/protein structures using molecular dynamics (MD) method is often associated with difficulties, because it is nearly impossible to observe spontaneous diffusion in MD experiments. In this work Molecular Dynamics (MD) and Umbrella Sampling (US) methods are used to study ion transport through 5-HT3 Serotonin receptor.

Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

[Molecular Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation of Formin mDial].

Steered molecular dynamics (SMD) was used to identify the interacting amino-acid residues on the surfaces of formin mDia1 domains for DID–DAD interactions, which is responsible for formin autoinhibition, and DID–Rho GTPase, which is responsible for formin activation. Ionic interactions between Glu178 and Arg248 and hydrophobic interactions between a carbon atom of Thr175 and the aromatic ring of Phe247 were the most stable. The DID–Rho interaction was the strongest, being mediated by triple ionic interactions of positively charged Rho residues with a DID amino-acid triplet, which included two negatively charged residues with an uncharged one between them. The DID sites binding with Rho and DAD overlap in part, but different DID amino-acid residues are involved in DID interactions with different partners. Conformational changes potentially arising in the formin domains upon activation or inactivation are discussed.