Research

Molecular origins of Muscle Contraction In order to describe muscle contraction we are developing a computational platform that incorporates current knowledge of molecular structure, biochemical energetics, and binding kinetics. This platform can be used to generate new mechanistic hypotheses concerning the functions of the contractile proteins and quantitatively evaluate the roles of accessory and regulatory proteins in muscle contraction. The model integrates recent advances in understanding of biochemical states of myosin and their transition rates, function of myosin molecular motors in sarcomere lattice, Ca²⁺ regulation of myosin binding, and actin and myosin filament extensibility. The quantitative modeling of contraction is ultimately essential for understanding of the molecular basis for a wide range of syndromes and diseases.

Multi-Scale Modeling Currently, only a few tools exist to investigate how, in an integrated framework, the mechanical environment influences biology (and vice versa) at the molecular, cellular and tissue scales. We are developing a computational platform that unites structure and function at molecular scale with higher-order organization and integrated physiological function. The resulting multi-scale model links biochemical kinetics and molecular organization to emergent mechanical properties and processes at hierarchical scales – spanning the molecular to tissue level. Using probabilistic and stochastic approaches to model protein binding kinetics, the model explicitly couples cell contractility and mechanics to adhesion: at an integrated molecular and cellular scale, and cellular and tissue scale.

Airway Narrowing In this study, we quantitatively examine mucosal folding and excessive narrowing in a contracting airway. The principal aim is to quantitatively determine deformation of the cell, and tractions between the cells, or between cell-extracellular matrix. The quantitative simulations provide: (i) linkage between underlying molecular processes, the geometry of the airway wall, and the airway hyperresponsiveness to contractile stimuli; (ii) the deformations experienced by tissues and single cells in the constricting airway; (iii) interfacial tractions (stresses) between the layers, especially at the points of extremely large deformation, and (iv) variations in stress and strain at the sub-cellular level. These points are critical to our understanding of the role of mechanical forces on regulation of signaling, gene expression, and fibrosis in the airway wall.

In vitro Model of Airway Narrowing Asthmatic subjects lack the bronchodilating response and bronchoprotective effects of deep inspirations. However, the underlying mechanisms of this behavior are not clear at the contractile protein or tissue levels. We developed an in vitro model of airway narrowing in order to quantitatively assess how and to what degree the observed alternations in airway smooth muscle cross-bridge kinetics and airway wall remodeling can account for the above clinical observations in asthma and COPD. The model simultaneously includes dynamics of breathing and various physiological levels of muscle activation.

Cell Adhesion It has been shown that the formation of adhesive complexes strengthens when mechanical force is applied to them. Furthermore, it has been experimentally demonstrated that force affects binding either by shortening bond lifetime – slip bond, or by prolonging bond lifetime – catch bond. We are developing the model of strain dependent binding of receptors to ligands. This model may mechanistically explain the above observations and elucidate important aspects of contraction-adhesion coupling and receptor-mediated regulation of cell functions in tissue, such as proliferation, adhesion, migration, differentiation, and cell death.

Traction Microscopy Quantification of contractility and adhesion of living cells in culture is essential in understanding of mechanotransduction in a variety of cell functions, including contraction, spreading, crawling, and wound healing. Using the deformable gel substrate technique, we measure displacements of small (0.2mm diameter) fluorescent beads during contraction of plated cell challenged by varying doses of contractile agent. The traction field is computed from the displacement field at the cell-gel interface. The average stress within the cell is calculated from the traction field. These findings are used for development of mechanistic models of cell function that emerge from collective interactions among different cytoskeletal filaments and extracellular adhesions in living cells.

Perturbed Equilibria of Myosin Binding In asthma, the mechanisms relating airway obstruction, hyperresponsiveness, and inflammation remain rather mysterious. The regulation of airway smooth muscle length and an airway diameter corresponds to a dynamically equilibrated steady state that requires a continuous supply of external mechanical energy (derived from tidal lung inflations) acting to perturb the interactions of myosin with actin, drives the molecular state of the system far away from thermodynamic equilibrium, and biases the muscle toward mechanically induced relaxation. This mechanism may help to elucidate several unexplained phenomena including the multifactorial origins of airway hyperresponsiveness, how allergen sensitization leads to airway hyperresponsiveness, how hyperresponsiveness can persist long after airway inflammation is resolved, and the inability of deep inspirations to relax airway smooth muscle in asthma.

Optical Magnetic Twisting Cytometry Magnetic twisting cytometry probes mechanical properties of an adherent cell by applying a torque to a magnetic bead tightly bound to the cell surface. Using a three-dimensional model of cell deformation we compute the relationships between the applied torque, and resulting bead rotation and lateral bead translation. From the analysis, we estimate the cell elastic modulus and the degree of the cell orthotropy, from the measurements of either bead rotations or lateral bead translations, if the degree of bead embedding and the cell height are known. Also, from these computations we estimate the adhesive forces between the bead and the cell surface.