research

Nikolai Smolin: research interests

home curriculum vitae research publications presentations links

Research interests

My interests include, but are not limited to: computational molecular biophysics, large-scale simulation and modeling of biomolecular systems, protein engineering, drug designe, homology modeling, developing scientific computational tools and software and education in scientific and high performance computing. My scientific interests lie in the broad area of molecular biophysics, at the interface of physics, biology and chemistry. Molecular biophysics seeks to understand what dynamic and structural properties are important to proteins’ functions. How does a given biomolecule work? What are the mechanisms of biochemical ‘nano-machines’? In particular, I am interested in understanding the physics and functions of biomolecules at the atomic level and the role of solvent in conformational behavior, dynamics, interactions, and aggregation of biomolecules, macromolecular crowding. To address these problems, I use high-performance computer simulation of complex biological macromolecules.

Coupling between Dynamics and Function of Proteins:

Motions in proteins play key roles in the functioning of the cell. A molecular-level understanding of how proteins function is of fundamental importance in biology and medicine. In recent years, research concerning the function of proteins has shifted emphasis towards dynamic behavior. Whereas formerly function was related almost exclusively to static protein structure, it is now realized that key steps in protein function frequently involve internal motions. Furthermore, large scale motions in proteins are essential for the function of enzymes, for example, enabling substrate and product entry and exit. Proteins, and in particular multi-domain proteins, share a structural complexity that is also reflected in a complex dynamical behavior. Understanding functions of these biomolecules is possible only if we know the structures and their dynamical properties. Few techniques are available that can directly probe large-scale protein motions. Among the most direct is molecular dynamics simulation in which, using an empirical potential energy function, the equations of motion of a system of atoms are solved numerically. In this way, detailed descriptions of protein motions can be explored for timescales up to about one microsecond. We demonstrated that combination of molecular dynamics simulation and neutron spin echo spectroscopy is a powerful combination which can characterize complex domain motions at atomic detail.

Cardiac Troponin Complex: The cardiac troponin I (cTnI) inhibitory peptide (IPcTnI) and N-terminal domains (NtcTnI) both regulate the affinity of troponin C (cTnC) to Ca being substrates for protein kinases -C (PKC; T143) and -A (PKA; S23/24), respectively. The R145W mutation localized next to the T143 site has been linked to the development of restrictive cardiomyopathy (RCM) which is associated with high morbidity and mortality. We hypothesized that R145W blocks the physiological crosstalk between NtcTnI and IPcTnI; this uncoupling may contribute to the RCM phenotype. Here, we employed the recombinant cardiac troponin complex (cTn) exchange to study the impact of the S23/24D and T143E phosphomimics and R145W mutations in human skinned ventricular myocardium on myofilament Ca2+ induced force responsiveness, ATPase rate, and single myofibril kinetics. To test our hypotheses we also performed molecular dynamics (MD) simulations of the same systems. In biophysical experiments T143E blunted the effects of S23/24D. In the presence of the R145W mutation, myofilament Ca sensitivity was dramatically elevated, independent of PKA pseudo-phosphorylation. MD simulations show changes in overall dynamics of cTn upon introducing mutations. We observed no changes in Ca coordination. In order to see if mutations are changing interactions between cTnI and cTnC, we computed contact maps and found that interaction pattern for mutated systems are different compared to wild-type. In particular, mutations are introducing a different contact network between cTn domains. We conclude that 1) in the absence of the R145W mutation there is a tight crosstalk between the NtcTnI and IPcTnI, whereby PKC signaling reciprocally inhibits the impact of PKA phosphorylation. 2) This crosstalk is interrupted by the R145W RCM-linked mutation and this molecular mechanism may underlie the cardiac pathogenesis of this mutation.

SERCA: Oscillations in free cytoplasmic Ca govern the relaxation and contraction of muscles. This Ca cycle is the result of the coordinated actions of channels in the sarcoplasmic reticulum (SR) membrane, which release Ca into the cytoplasm during contraction, and the SR calcium pump (SERCA) 1, which transports Ca2+ ions back into the SR to allow muscle relaxation. In the heart, disordered SERCA expression, function, and regulation are linked to cardiac disease, motivating investigation of SERCA structure/function mechanisms as a path to new therapeutic interventions. One important aspect of SERCA function is the large amplitude conformational changes that occur during the transport cycle. To characterize the conformational dynamics of sarcoplasmic reticulum (SR) calcium pump (SERCA) we performed molecular dynamics simulations beginning with several different high-resolution structures. We quantified differences in structural disorder and dynamics for an open conformation of SERCA versus closed structures, and observed that dynamic motions of SERCA cytoplasmic domains decreased with decreasing domain-domain separation distance. The results are useful for interpretation of recent intramolecular Förster resonance energy transfer (FRET) distance measurements obtained for SERCA fused to fluorescent protein tags. Those previous physical measurements revealed several discrete structural substates and suggested open conformations of SERCA are more dynamic than compact conformations. The present simulations support this hypothesis and provide additional details of SERCA molecular mechanisms. Specifically, all-atoms simulations revealed large-scale translational and rotational motions of the SERCA N-domain relative to the A- and P-domains during the transition from an open to a closed headpiece conformation over the course of a 400 ns trajectory. The open-to-closed structural transition was accompanied by a disorder-to-order transition mediated by an initial interaction of an N-domain loop (Nβ5-β6, residues 426-436) with residues 133-139 of the A-domain. Mutation of three negatively charged N-domain loop residues abolished the disorder-to-order transition, and prevented the initial domain-domain interaction and subsequent closure of the cytoplasmic headpiece. Coarse-grained molecular dynamics simulations were in harmony with all-atoms simulations and physical measurements, and revealed a close communication between fluorescent protein tags and the domain to which they were fused. The data indicate that previous intramolecular FRET distance measurements report SERCA structure changes with high fidelity, and suggest a structural mechanism that facilitates the closure of the SERCA cytoplasmic headpiece.

Phospholamban: Heart failure is a leading cause of mortality, affecting an estimated 26 million people worldwide, and up to 6 million people in the US. Dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) are the primary causes of heart failure, and are often associated with mutations in genes encoding cardiac Ca2+ handling proteins including phospholamban (PLB). PLB is a homopentameric, integral sarcoplasmic reticulum (SR) membrane protein, which upon deoligomerization into active monomers reversibly inhibits SR Ca2+ ATPase (SERCA), thereby directly regulating cardiac Ca2+ kinetics and contractility. A naturally occurring missense mutation in PLB, caused by substitution of a stop codon for Leu-39 (L39X) has been shown to dysregulate SR Ca2+ cycling and contractility by acting as PLB null in humans, resulting in hereditary DCM, HCM, heart failure and premature death. All atom molecular dynamics simulations were performed to evaluate the stability and membrane topology of WT and mutant PLB pentamers. 100 ns post-equilibration time trajectories revealed changes in RMSD, van der Waals and electrostatic interactions, hydrogen bonding, and the degree of displacement of the TM helix from the lipid bilayer. The RMSD of Cα atoms of the heart failure truncation mutant L39X was markedly increased compared to WT, which consistently showed a stable structure with little deviation from the NMR solution. Figure shows that L39X lacks van der Waals and Coulombic interactions needed for stabilizing the PLB oligomer compared to WT. Significantly, while the TM domain of the WT protein is retained in the bilayer, the L39X mutant TM domain translocated out of the bilayer within a few ns, and is fully solubilized by the end of the simulation

    • Advanced Molecular Simulation of molecular/macromolecular systems: Application of state-of-the-art computer simulation techniques including Molecular dynamics (MD), Brownian dynamics (BD) and Coarse Grained (CG) modeling to probe the structures, dynamics, functions, interactions of proteins and their complexes.
    • Protein Engineering: Application of the knowledge obtained from molecular simulations to guide protein engineering.
    • Interpretation of Fluorescence Resonance Energy Transfer (FRET) experiments (SERCA, sodium pump, PLB oligomerization, etc.) using molecular dynamics simulation.
    • Protein PEGylation
    • Nanoscale Biophysics
    • Neutron scattering in biology: Simulation and experiment
    • Determine the effects of different antifreeze proteins on ice formation, as well as mutants that abolish activity. MD studies of osmolytes and their effect on ice formation both alone and in combination with antifreeze proteins
    • Effects of high hydrostatic pressure, temperature and cosolvents on the structure and dynamic of proteins and its solvent
    • Structural and dynamic properties of hydration water. Hydrogen bonded network of hydration water at the biomolecular surfaces. Formation of spanning water networks on protein surfaces via 2D percolation transition
    • Structure-dynamics-function relationships of the protein-water system
    • The analyze of short-range-order atomic structure of liquid metals by Voronoi polyhedron method and checkout of an adequacy of the results gained by the RMC method

"...everything that living things do can be understood in terms of the jigglings and wigglings of atoms" ( Richard Feynman, Lectures in Physics )