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Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…
In this work we monitor the catalytic mechanism of P-glycoprotein (Pgp) using single-molecule fluorescence resonance energy transfer (FRET). Pgp, a member of the ATP binding cassette family of transport proteins, is found in the plasma…
While allostery is of paramount importance for protein signaling and regulation, the underlying dynamical process of allosteric communication is not well understood. PDZ3 domain represents a prime example of an allosteric single-domain…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
Bending rigidity of a charged membrane or a charged polyelectrolyte screened by monovalent counterions is known to be enhanced by electrostatic effects. We show that in the case of screening by multivalent counterions the electrostatic…
Charge regulation is an important aspect of electrostatics in biological and colloidal systems, where the charges are generally not fixed, but depend on the environmental variables. Here, we analyze the charge regulation mechanism in…
We demonstrate anisotropic photostriction in two-dimensional orthorhombic semiconductors using time-dependent density functional theory. By tracing the dynamics of photoexcited carriers, we establish a quantitative link between carrier…
Protein electrostatic states have been demonstrated to play crucial roles in catalysis, ligand binding, protein stability, and in the modulation of allosteric effects. Electrostatic states are demonstrated to appear conserved among DEAD-box…
RSC is an essential chromatin remodeling factor that is required for the control of several processes including transcription, repair and replication. The ability of RSC to relocate centrally positioned mononucleosomes at the end of…
Random polyampholytes (PAs) contain positively and negatively charged monomers that are distributed randomly along the polymer chain. The interaction between charges is assumed to be given by the Debye-Huckel potential. We show that the…
Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. They describe the response a complex to binding of ligands at sites that are spatially well separated from the binding region. We…
The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…
Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone modification dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include…
There is compelling evidence that substrate stiffness affects cell adhesion as well as cytoskeleton organization and contractile activity. This work was designed to study the cytoskeletal contractile activity of cells plated on microposts…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular…