Extensive research in last a few decades provided large amount of data from animal and human studies related to many complex diseases. The data were collected at different length scales spanning genetics, protein interactions and structure, and cell, tissue and organ function. Most of the findings at any scale were directly connected to particular disease, neglecting processes at different scales that can significantly distort outcome at organ function. This partial approach led to expensive and frequently unsuccessful development of new drugs and therapies.
Unifying Concepts of the Generalized Sliding Filament Model (MUSICO)
Computational platform MUSICO (MUscle SImulation COde) for modelling realistic sarcomeric system has been developed with the aim to simulate a wide variety of experimental muscle behavior. The platform offers a modular program structure that allows extension and replacement of any part of sarcomeric system (calcium activation, cross-bridge cycle, sarcomere geometry, etc.). The current version of the MUSICO involves a number of sarcomere geometry models including the three-dimensional spatial models of multi-sarcomere geometry. Furthermore, multiple actomyosin cycle models and calcium regulatory models are also incorporated. Nonlinear mechanical behavior of extensible filaments and crossbridges is addressed using iterative finite element scheme. Moreover, in order to speed-up simulations, the platform is provided with parallelized computational algorithm.
MUSICO physiological model integrates the kinetics of actomyosin interactions and the action of regulatory proteins with extensible sliding filament models.
The principal goal of the computational mechanobiology lab is to develop a tool for the quantitative analysis of structure-function relationship in muscle over multiple length scales. Inferring disease pathophysiology from molecular dysfunction we have developed the computational platform MUSICO (Muscle Simulation Code), to enable translating structural or functional abnormalities at the nano-scale into abnormalities at the scale of the organ and organ systems.
Multiscale Models of Skeletal and Cardiac Muscle
We were inspired by new discoveries and initiated development of multiscale models by revising the basic models of muscle contraction by, for example including myofilament extensibility, and developing the models of organs using newly developed multiscale approaches. These new approaches include crossbidge kinetics, thin filament regulation and mesoscale orientation muscle fibers from diffusion spectrum magnetic resonance imaging. The software developed in the lab provides opportunities for applications in surgical planning and personalized evaluation of patient’s loss of performance in disease or with age.
Thin Filament Regulation by Calcium
The contractility of striated muscle is regulated by calcium dependent azimuthal movements of tropomyosin-troponin complexes over the surface of the actin filament. Calcium regulation of muscle contraction is essential for modulating impaired muscle function in most of neuromuscular diseases. We have developed the most comprehensive models of calcium regulation that allow translation of data from the experiments in solution to contractility of muscle fibers and whole muscles.
Smooth Muscle Contraction and Regulation
The flow patterns in tubular organs are modulated by the mechanical forces acting on airway or vessel walls and causing change in their size. In order to predict realistic behavior of tubular organs under dynamic loading conditions and in the presence of active muscle force we have developed a molecular model of smooth muscle (SM) contraction including the SM regulation by calcium. As an application of this computational model we have developed a computational model of airway narrowing. These models could lead to future development of virtual lungs or other virtual tubular organs containing smooth muscle.
Neuromuscular Disease Assessment and Therapy
For monitoring health improvement or disease progression in patients with a variety of neuromuscular disorders, ranging from amyotrophic lateral sclerosis to muscular dystrophy, the development or refining muscle assessment tools is necessary. In collaboration with Dr. Rutkove, this ongoing project aims to achieve strong theory and observed data connecting muscle impedance measurements and the pathological characteristics of tissue. For example non-invasive impedance data that can be used to characterize muscle histology; impedance-based imaging systems for the real-time evaluation of muscle contractile properties; and development of effective electrical muscle stimulation technology to serve as a useful means to improving muscle condition and health. When fully developed the impedance imaging system will enable muscle health assessment during muscle contraction in real time.
X-ray Diffraction in Living Cells
Small-angle X-ray diffraction is the only technique that can provide molecular level structural information from muscle tissue under hydrated, physiological conditions at the physiologically relevant millisecond time scale. The availability of spectacular quality diffraction data currently provides only limited amount of extracted information due to lack of suitable analysis and modeling tools. Newly developed tools using data from MUSICO simulations provide a novel way of extracting new information from monitoring interactions at molecular scale and muscle contractile response at macroscopic scale. For example, this approach provided, for the first time, measurement of forces acting on actin filaments in leaving cells. Continuous development of these tools is vital to allow extraction of maximum information from the X-ray data and provide the precise information about the changes in myofilament structure and function associated with myopathic diseases.
MD Simulation of Molecular Elasticity
Understanding the sub-molecular basis of crossbridge elasticity provides the foundations for the mechano-chemistry of the acto-myosin cycle, in particular, the energetics of the power stroke, the possible asymmetry of the energy landscape, and strain dependent myosin binding in the 3D sarcomere lattice. The elasticity of cross-bridge components (the myosin lever arm, the neck and the coiled coil (S2) domains) can be assessed all-atom molecular dynamics (MD) simulations. This ongoing process is updated with new atomic structures of the crossbridge components as they appear. Also, the unresolved structures, e.g. the myosin “neck' region that separates the S1 & S2 domains, can be assessed by modeling it as random chains connecting a single coil of the lever arm(s) with coiled-coil of S2 region using MD simulations. So far we have assessed the stability of the relatively simple coiled-coil by MD simulations over several ns. Overall, this approach can be used to reveal how minor differences in sequences of the S2, lever arm and neck region affect the crossbridge elasticity. Using similar MD modeling methodology, we are working on assessing the elasticity of tropomyosins and, in collaboration with Dr. Regnier’s lab, the effect of cTnI mutations on structure-function of cardiac troponin.