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The catalytic conversion of ATP and AMP to ADP by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of LID and NMP domains, during the repeated catalytic cycle. We discover…
The cooperative action of many molecular motors is essential for dynamic processes such as cell motility and mitosis. This action can be studied by using motility assays in which the motion of cytoskeletal filaments over a surface coated…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
We present a study on filamentous actin solutions containing heavy meromyosin subfragments of myosin II motor molecules. We focus on the viscoelastic phase behavior and internal dynamics of such networks during ATP depletion. Upon…
The rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent feature to reveal high coordination among multiple chemical sites on the stator F1 ring, which also contributes to tight coupling between the chemical reaction…
Biophysical models are often populated by a large number of input parameters that are difficult to predict or measure experimentally. The validity and robustness of a given model can be evaluated by a sensitivity test to its input…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Immune cells recognize and discriminate antigens through immunological synapses - dynamic intercellular junctions exhibiting highly organized receptor-ligand patterns. While much work has focused on molecular kinetics and passive mechanisms…
The actin cortex of an animal cell is a thin polymeric layer attached to the inner side of the plasma membrane. It plays a key role in shape regulation and pattern formation on the cellular and tissue scale and, in particular, generates the…
The synthetic actin network arouses great interest as bio-material due to its soft and wet nature that mimics many biological scaffolding structures. Inside the cell, the actin network is regulated by tens of actin-binding proteins (ABP's),…
In yeast (Saccharomyces cerevisiae) and plant roots (Arabidopsis thaliana) zinc enters the cells via influx transporters of the ZIP family. Since zinc is both essential for cell function and toxic at high concentrations, tight regulation is…
Regulation of contraction in striated muscle is controlled by a dual mechanism involving both thin filaments containing actin and thick filaments containing myosin. The thin filament is activated by calcium ions binding to troponin, leading…
Associative polymers (APs) with reversible, specific interactions between ``sticker'' sites exhibit a phase behavior that depends on a delicate balance between distinct contributions controlling the binding. For highly-bonded systems, it is…
Protein-protein interactions are the basis of many important physiological processes and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitor of apoptosis proteins (IAPs)-mediated interactions are…
Analyzing kinetic experiments on protein aggregation using integrated rate laws has led to numerous advances in our understanding of the fundamental chemical mechanisms behind amyloidogenic disorders such as Alzheimer's and Parkinson's…
Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the…
Experimental observations on synaptic plasticity at individual glutamatergic synapses from the CA3 Shaffer collateral pathway onto CA1 pyramidal cells in the hippocampus suggest that the transitions in synaptic strength occur among discrete…
Actin is a globular protein which forms long filaments in the eukaryotic cytoskeleton, whose roles in cell function include structural support, contractile activity to intracellular signalling. We model actin filaments as two chains of…
Analytical research of results of experimental and theoretical studies on pathogenesis of psoriatic disease is carried out. The new model of pathogenesis - skin reaction to systemic psoriatic process SPP is formulated. ... Psoriatic…
Predicting the kinetics of drug-protein interactions is crucial for understanding drug efficacy, particularly in personalized medicine, where protein mutations can significantly alter drug residence times. This study applies Replica…