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Venkaiah Betapudi - One of the best experts on this subject based on the ideXlab platform.

  • Non-muscle myosin II Motor Proteins in human health and diseases
    Genome Analysis and Human Health, 2017
    Co-Authors: Venkaiah Betapudi
    Abstract:

    Man-made machines mediate a diverse range of human activities in modern world, so are natural myosin Motor Proteins in driving multiple aspects of cellular life. Myosins belong to a special group of Proteins called mechanochemical enzymes or colloquially molecular machines/Motor Proteins because of their ability to move on intracellular tracks and convert cellular free energy released from ATP into mechanical work. Every cell in the human body is equipped with polymerization, cytoskeletal, rotary, nucleic acid, myosin III, and prestin type Motor Proteins. These molecular machines with cell-specific expression perform dedicated functions perhaps as a part of nature’s strategy for cell origin and diversification. The mechanical work performed by these cellular Motor Proteins intersects with every facet of cell biology. Indeed, these Motor Proteins drive several cellular activities that are essential for mediating reproduction, childbirth, growth, development, immunity, and singing a courtship song in fruit flies as well as predisposing human beings to a certain degree of risk for various pathological conditions and diseases. No biological cell can function and operate without the involvement of these multifunctional molecular machines. The present chapter is about the discovery, current understanding, and recent advances in various aspects of myosin Motor Proteins as well as their regulation and relevance to human health and diseases.

  • Life without double-headed non-muscle myosin II Motor Proteins.
    Frontiers in Chemistry, 2014
    Co-Authors: Venkaiah Betapudi
    Abstract:

    Non-muscle myosin II Motor Proteins (myosin IIA, myosin IIB, and myosin IIC) belong to a class of molecular Motor Proteins that are known to transduce cellular free-energy into biological work more efficiently than man-made combustion engines. Nature has given a single myosin II Motor protein for lower eukaryotes and multiple for mammals but none for plants in order to provide impetus for their life. These specialized nanomachines drive cellular activities necessary for embryogenesis, organogenesis, and immunity. However, these multifunctional myosin II Motor Proteins are believed to go awry due to unknown reasons and contribute for the onset and progression of many autosomal-dominant disorders, cataract, deafness, infertility, cancer, kidney, neuronal, and inflammatory diseases. Many pathogens like HIV, Dengue, hepatitis C, and Lymphoma viruses as well as Salmonella and Mycobacteria are now known to take hostage of these dedicated myosin II Motor Proteins for their efficient pathogenesis. Even after four decades since their discovery, we still have a limited knowledge of how these Motor Proteins drive cell migration and cytokinesis. We need to enrich our current knowledge on these fundamental cellular processes and develop novel therapeutic strategies to fix mutated myosin II Motor Proteins in pathological conditions. This is the time to think how to relieve the hijacked myosins from pathogens in order to provide a renewed impetus for patients' life. Understanding how to steer these molecular Motors in proliferating and differentiating stem cells will improve stem cell based-therapeutics development. Given the plethora of cellular activities non-muscle myosin Motor Proteins are involved in, their importance is apparent for human life.

  • myosin ii Motor Proteins with different functions determine the fate of lamellipodia extension during cell spreading
    PLOS ONE, 2010
    Co-Authors: Venkaiah Betapudi
    Abstract:

    Non-muscle cells express multiple myosin-II Motor Proteins myosin IIA, myosin IIB and myosin IIC transcribed from different loci in the human genome. Due to a significant homology in their sequences, these ubiquitously expressed myosin II Motor Proteins are believed to have overlapping cellular functions, but the mechanistic details are not elucidated. The present study uncovered a mechanism that coordinates the distinctly localized myosin IIA and myosin IIB with unexpected opposite mechanical roles in maneuvering lamellipodia extension, a critical step in the initiation of cell invasion, spreading, and migration. Myosin IIB Motor protein by localizing at the front drives lamellipodia extension during cell spreading. On the other hand, myosin IIA localizes next to myosin IIB and attenuates or retracts lamellipodia extension. Myosin IIA and IIB increase cell adhesion by regulating focal contacts formation in the spreading margins and central part of the spreading cell, respectively. Spreading cells expressing both myosin IIA and myosin IIB Motor Proteins display an organized actin network consisting of retrograde filaments, arcs and central filaments attached to focal contacts. This organized actin network especially arcs and focal contacts formation in the spreading margins were lost in myosin IIÂ cells. Surprisingly, myosin IIB cells displayed long parallel actin filaments connected to focal contacts in the spreading margins. Thus, with different roles in the regulation of the actin network and focal contacts formation, both myosin IIA and IIB determine the fate of lamellipodia extension during cell spreading.

Stefan Diez - One of the best experts on this subject based on the ideXlab platform.

  • challenges in estimating the motility parameters of single processive Motor Proteins
    Biophysical Journal, 2017
    Co-Authors: Felix Ruhnow, Linda Kloβ, Stefan Diez
    Abstract:

    Abstract Cytoskeletal Motor Proteins are essential to the function of a wide range of intracellular mechano-systems. The biophysical characterization of their movement along their filamentous tracks is therefore of large importance. Toward this end, single-molecule, in vitro stepping-motility assays are commonly used to determine Motor velocity and run length. However, comparing results from such experiments has proved difficult due to influences from variations in the experimental conditions and the data analysis methods. Here, we investigate the movement of fluorescently labeled, processive, dimeric Motor Proteins and propose a unified algorithm to correct the measurements for finite filament length as well as photobleaching. Particular emphasis is put on estimating the statistical errors associated with the proposed evaluation method, as knowledge of these values is crucial when comparing measurements from different experiments. Testing our approach with simulated and experimental data from GFP-labeled kinesin-1 Motors stepping along immobilized microtubules, we show 1) that velocity distributions should be fitted by a t location-scale probability density function rather than by a normal distribution; 2) that the impossibility to measure events shorter than the image acquisition time needs to be taken into account; 3) that the interaction time and run length of the Motors can be estimated independent of the filament length distribution; and 4) that the dimeric nature of the Motors needs to be considered when correcting for photobleaching. Moreover, our analysis reveals that controlling the temperature during the experiments with a precision below 1 K is of importance. We believe our method will not only improve the evaluation of experimental data, but also allow for better statistical comparisons between different populations of Motor Proteins (e.g., with distinct mutations or linked to different cargos) and filaments (e.g., in distinct nucleotide states or with different posttranslational modifications). Therefore, we include a detailed workflow for image processing and analysis (including MATLAB code), serving as a tutorial for the estimation of motility parameters in stepping-motility assays.

  • challenges in estimating the motility parameters of single processive Motor Proteins
    bioRxiv, 2017
    Co-Authors: Felix Ruhnow, Linda Kloβ, Stefan Diez
    Abstract:

    Cytoskeletal Motor Proteins are essential to the function of a wide range of intracellular mechano-systems. The biophysical characterization of their movement along their filamentous tracks is therefore of large importance. Towards this end, single-molecule, in vitro stepping-motility assays are commonly used to determine Motor velocity and run length. However, comparing results from such experiments has proved difficult due to influences from variations in the experimental conditions and the data analysis methods. Here, we investigate the movement of fluorescently-labeled, processive, dimeric Motor Proteins and propose a unified algorithm to correct the measurements for finite filament length as well as photobleaching. Particular emphasis is put on estimating the statistical errors associated with the proposed evaluation method as knowledge of these values is crucial when comparing measurements from different experiments. Testing our approach with simulated and experimental data from GFP-labeled kinesin-1 Motors stepping along immobilized microtubules, we show (i) that velocity distributions should be fitted by a t location-scale probability density function rather than by a normal distribution, (ii) that the impossibility to measure events shorter than the image acquisition time needs to be accounted for, (iii) that the interaction time and run length of the Motors can be estimated independent of the filament length distribution, and (iv) that the dimeric nature of the Motors needs to be considered when correcting for photobleaching. Moreover, our analysis reveals that controlling the temperature during the experiments with a precision below 1 K is of importance. We believe, our method will not only improve the evaluation of experimental data, but will also allow for better statistical comparisons between different populations of Motor Proteins (e.g. with distinct mutations or linked to different cargos) and filaments (e.g. in distinct nucleotide states or with different posttranslational modifications).

  • Measurements of Single Fluorescent Motor Proteins: The Right Way
    Biophysical Journal, 2014
    Co-Authors: Felix Ruhnow, Linda Kloβ, Stefan Diez
    Abstract:

    Cytoskeletal Motor Proteins are required in many cellular processes, such as intracellular transport and mitosis. Therefore, the biophysical characterization of Motor protein movement along their filamentous tracks is essential. Commonly, stepping motility assays are used to determine the stepping and detachment rates of various molecular Motor Proteins by measuring their speed, run length and interaction time. However, comparison of these results proved to be difficult because the experimental setup (e.g. bead assay vs. single-molecule fluorescence assay), the experimental conditions (e.g. temperature, buffer or filament preparation) and data analysis (e.g. normal vs. exponential distribution) can influence the results. Here, we describe a method to evaluate traces of fluorescent Motor Proteins and propose an algorithm to correct the measurements for photobleaching and the limited length of the filaments. Additionally, bootstrapping is used to estimate statistical errors of the evaluation method. The method was tested with numerical simulations as well as with experimental data from kinesin-1 stepping experiments to show that the run length of kinesin-1 is independent of the microtubule length distribution. Our work will not only improve the evaluation of experimental data, but will also allow for better statistical comparison of two or more populations of Motor Proteins (e.g. Motors with distinct mutations or Motors linked to different cargos).

  • towards the application of cytoskeletal Motor Proteins in molecular detection and diagnostic devices
    Current Opinion in Biotechnology, 2010
    Co-Authors: Till Korten, Alf Månsson, Stefan Diez
    Abstract:

    Over the past ten years, great advancements have been made towards using biomolecular Motors for nanotechnological applications. In particular, devices using cytoskeletal Motor Proteins for molecular transport are maturing. First efforts towards designing such devices used Motor Proteins attached to micro-structured substrates for the directed transport of microtubules and actin filaments. Soon thereafter, the specific capture, transport and detection of target analytes like viruses were demonstrated. Recently, spatial guiding of the gliding filaments was added to increase the sensitivity of detection and allow parallelization. Whereas molecular Motor powered devices have not yet demonstrated performance beyond the level of existing detection techniques, the potential is great: Replacing microfluidics with transport powered by molecular Motors allows integration of the energy source (ATP) into the assay solution. This opens up the opportunity to design highly integrated, miniaturized, autonomous detection devices. Such devices, in turn, may allow fast and cheap on-site diagnosis of diseases and detection of environmental pathogens and toxins.

  • stretching and transporting dna molecules using Motor Proteins
    Nano Letters, 2003
    Co-Authors: Stefan Diez, Cordula Reuther, Cerasela Zoica Dinu, Ralf Seidel, Michael Mertig, Wolfgang Pompe, Jonathon Howard
    Abstract:

    Inside cells, Motor Proteins perform a variety of complex tasks including the transport of vesicles and the separation of chromosomes. We demonstrate a novel use of such biological machines for the mechanical manipulation of nanostructures in a cell-free environment. Specifically, we show that purified kinesin Motors in combination with chemically modified microtubules can transport and stretch individual λ-phage DNA molecules across a surface. This technique, in contrast to existing ones, enables the parallel yet individual manipulation of many molecules and may offer an efficient mechanism for assembling multidimensional DNA structures.

Viola Vogel - One of the best experts on this subject based on the ideXlab platform.

  • molecular shuttles based on Motor Proteins active transport in synthetic environments
    Reviews in Molecular Biotechnology, 2001
    Co-Authors: Henry Hess, Viola Vogel
    Abstract:

    Abstract Active transport in cells, utilizing molecular Motors like kinesin and myosin, provides the inspiration for the integration of active transport into synthetic devices. Hybrid devices, employing Motor Proteins in a synthetic environment, are the first prototypes of molecular shuttles. Here the basic characteristics of Motor Proteins are discussed from an engineering point of view, and the experiments aimed at incorporating Motor Proteins, such as myosins and kinesins, into devices are reviewed. The key problems for the construction of a molecular shuttle are: guiding the direction of motion, controlling the speed, and loading and unloading of cargo. Various techniques, relying on surface topography and chemistry as well as flow fields and electric fields, have been developed to guide the movement of molecular shuttles on surfaces. The control of ATP concentration, acting as a fuel supply, can serve as a means to control the speed of movement. The loading process requires the coupling of cargo to the shuttle, ideally by a strong and specific link. Applications of molecular shuttles can be envisioned, e.g. in the field of nano-electro-mechanical systems (NEMS), where scaling laws favor active transport over fluid flow, and in the bottom-up assembly of novel materials.

  • Light-Controlled Molecular Shuttles Made from Motor Proteins Carrying Cargo on Engineered Surfaces
    Nano Letters, 2001
    Co-Authors: Henry Hess, John Clemmens, Dong Qin, Jonathon Howard, Viola Vogel
    Abstract:

    Molecular shuttles have been built from Motor Proteins capable of moving cargo along engineered paths. We illustrate alternative methods of controlling the direction of motion of microtubules on engineered kinesin tracks, how to load cargo covalently to microtubules, and how to exploit UV-induced release of caged ATP combined with enzymatic ATP degradation by hexokinase to turn the shuttles on and off sequentially. These are the first steps in the development of a tool kit to utilize molecular Motors for the construction of nanoscale assembly lines.

Jonathon Howard - One of the best experts on this subject based on the ideXlab platform.

  • Functional surface attachment in a sandwich geometry of GFP-labeled Motor Proteins.
    Single Molecule Enzymology, 2011
    Co-Authors: Volker Bormuth, Felix Zörgibel, Erik Schäffer, Jonathon Howard
    Abstract:

    Molecular Motors perform work in cells by moving in an ATP-dependent manner along filamentous tracks. In vitro, the mechanical action of such Motor Proteins can be investigated by attaching the molecules to surfaces in the so-called gliding or bead assays. Surface attachment protocols have to be used that do not interfere with the function of the molecule. Here, we describe a sandwich protocol that preserves functionality. The protocol can be used for a large variety of Proteins, in particular kinesin Motor Proteins that are GFP-tagged.

  • Motor Proteins as Nanomachines: The Roles of Thermal Fluctuations in Generating Force and Motion
    Biological Physics, 2010
    Co-Authors: Jonathon Howard
    Abstract:

    Motor Proteins are enzymes that convert chemical energy derived from the hydrolysis of a small molecule called ATP into mechanical work used to power directed movement along cytoskeletal filaments inside cells. Motor Proteins have essential biological functions such as driving the contraction of muscle, the beating of sperm and cilia, and the transport of intracellular cargoes. Motor Proteins are also interesting from a physical point of view because they do what no man-made engines do: they transduce chemical energy directly to mechanical work without using heat or electrical energy as an intermediate. A central issue in the mechanism of this chemomechanical transduction by Motor Proteins concerns the roles played by thermal fluctuations, diffusion and Brownian motion. In this lecture I discuss several molecular models for Motor Proteins, including so-called ratchet models, and compare predictions of these models to experimental results for the microtubule-based Motor protein kinesin. I argue that kinesin, which has two Motor domains or “heads,” walks using a “hand-over-hand” mechanism such that at least one head is bound to the microtubule. Diffusion likely plays an essential role by facilitating the search of the unbound head for the next binding site, a distance 8 nm away. During this diffusive phase, the bound head supports the load ensuring that forward motion can still take place even against loads up to several piconewtons.

  • stretching and transporting dna molecules using Motor Proteins
    Nano Letters, 2003
    Co-Authors: Stefan Diez, Cordula Reuther, Cerasela Zoica Dinu, Ralf Seidel, Michael Mertig, Wolfgang Pompe, Jonathon Howard
    Abstract:

    Inside cells, Motor Proteins perform a variety of complex tasks including the transport of vesicles and the separation of chromosomes. We demonstrate a novel use of such biological machines for the mechanical manipulation of nanostructures in a cell-free environment. Specifically, we show that purified kinesin Motors in combination with chemically modified microtubules can transport and stretch individual λ-phage DNA molecules across a surface. This technique, in contrast to existing ones, enables the parallel yet individual manipulation of many molecules and may offer an efficient mechanism for assembling multidimensional DNA structures.

  • mechanics of Motor Proteins and the cytoskeleton
    2001
    Co-Authors: Jonathon Howard, R. L. Clark
    Abstract:

    Preface - Introduction - PART I: PHYSICAL PRINCIPLES - Mechanical Forces - Mass, Stiffness, and Damping of Proteins - Thermal Forces and Diffusion - Chemical Forces - Polymer Mechanics - PART II: CYTOSKELETON - Structures of Cytoskeletal Filaments - Mechanics of the Cytoskeleton - Polymerization of Cytoskeletal Filaments - Force Generation by Cytoskeletal Filaments - Active Polymerization - PART III: Motor Proteins - Structures of Motor Proteins - Speeds of Motors - ATP Hydrolysis - Steps and Forces - Motility Models: From Crossbridges to Motion - Afterword - Appendix - Bibliography - Index

  • Light-Controlled Molecular Shuttles Made from Motor Proteins Carrying Cargo on Engineered Surfaces
    Nano Letters, 2001
    Co-Authors: Henry Hess, John Clemmens, Dong Qin, Jonathon Howard, Viola Vogel
    Abstract:

    Molecular shuttles have been built from Motor Proteins capable of moving cargo along engineered paths. We illustrate alternative methods of controlling the direction of motion of microtubules on engineered kinesin tracks, how to load cargo covalently to microtubules, and how to exploit UV-induced release of caged ATP combined with enzymatic ATP degradation by hexokinase to turn the shuttles on and off sequentially. These are the first steps in the development of a tool kit to utilize molecular Motors for the construction of nanoscale assembly lines.

Anatoly B. Kolomeisky - One of the best experts on this subject based on the ideXlab platform.

  • Theoretical Analysis of Run Length Distributions for Coupled Motor Proteins
    The Journal of Physical Chemistry B, 2019
    Co-Authors: Qian Wang, Anatoly B. Kolomeisky
    Abstract:

    Motor Proteins, also known as biological molecular Motors, play important roles in various biological processes. In recent years, properties of single-Motor Proteins have been intensively investiga...

  • Theoretical Investigations of the Role of Mutations in Dynamics of Kinesin Motor Proteins.
    The Journal of Physical Chemistry B, 2018
    Co-Authors: Mikita Misiura, Qian Wang, Margaret S. Cheung, Anatoly B. Kolomeisky
    Abstract:

    Motor Proteins are active enzymatic molecules that are critically important for a variety of biological phenomena. It is known that some neurodegenerative diseases are caused by specific mutations in Motor Proteins that lead to their malfunctioning. Hereditary spastic paraplegia is one of such diseases, and it is associated with the mutations in the neuronal conventional kinesin gene, producing the decreased speed and processivity of this Motor protein. Despite the importance of this problem, there is no clear understanding on the role of mutations in modifying dynamic properties of Motor Proteins. In this work, we investigate theoretically the molecular basis for negative effects of two specific mutations, N256S and R280S, on the dynamics of kinesin Motor Proteins. We hypothesize that these mutations might accelerate the adenosine triphosphate (ATP) release by increasing the probability of open conformations for the ATP-binding pocket. Our approach is based on the use of coarse-grained structure-based mo...

  • Theoretical Investigations of the Role of Mutations in Dynamics of Kinesin Motor Proteins B
    The Journal of Physical Chemistry, 2018
    Co-Authors: Mikita Misiura, Qian Wang, Margaret S. Cheung, Anatoly B. Kolomeisky
    Abstract:

    Motor Proteins are active enzymatic molecules that are critically important for a variety of biological phenomena. It is known that some neurodegenerative diseases are caused by specific mutations in Motor Proteins that lead to their malfunctioning. Hereditary spastic paraplegia is one of such diseases, and it is associated with the mutations in the neuronal conventional kinesin gene, producing the decreased speed and processivity of this Motor protein. Despite the importance of this problem, there is no clear understanding on the role of mutations in modifying dynamic properties of Motor Proteins. In this work, we investigate theoretically the molecular basis for negative effects of two specific mutations, N256S and R280S, on the dynamics of kinesin Motor Proteins. We hypothesize that these mutations might accelerate the adenosine triphosphate (ATP) release by increasing the probability of open conformations for the ATP-binding pocket. Our approach is based on the use of coarse-grained structure-based molecular dynamics simulations to analyze the conformational changes and chemical transitions in the kinesin molecule, which is also supplemented by investigation of a mesoscopic discrete-state stochastic model. Computer simulations suggest that mutations N256S and R280S can decrease the free energy difference between open and closed biochemical states, making the open conformation more stable and the ATP release faster, which is in agreement with our hypothesis. Furthermore, we show that in the case of N256S mutation, this effect is caused by disruption of interactions between α helix and switch I and loop L11 structural elements. Our computational results are qualitatively supported by the explicit analysis of the discrete-state stochastic model.

  • Motor Proteins and Molecular Motors
    2015
    Co-Authors: Anatoly B. Kolomeisky
    Abstract:

    Introduction Motor Proteins IN BIOLOGICAL SYSTEMS SINGLE-MOLECULE EXPERIMENTS DISCUSSION OF THEORETICAL MODELS FOR MOLECULAR MotorS Motor Proteins AS NANOSCALE MACHINES OUTLOOK Basic Properties of Motor Proteins HISTORY OF Motor Proteins CLASSIFICATION OF BIOLOGICAL MOLECULAR MotorS STRUCTURES OF Motor Proteins BIOLOGICAL FUNCTIONS OF MOLECULAR MotorS SUMMARY Experimental Studies of Motor Proteins INTRODUCTION BULK CHEMICAL-KINETIC MEASUREMENTS STRUCTURAL STUDIES SINGLE-MOLECULE FORCE SPECTROSCOPY FLUORESCENT LABELING AND SUPER-RESOLUTION TECHNIQUES MAJOR EXPERIMENTAL OBSERVATIONS SUMMARY Fundamental Physical Concepts: Equilibrium Approaches INTRODUCTION BASIC EQUILIBRIUM THERMODYNAMICS BASIC STATISTICAL MECHANICS APPLICATION FOR Motor Proteins SUMMARY Fundamental Physical Concepts: Non-Equilibrium Approaches INTRODUCTION MACROSCOPIC CHEMICAL KINETICS RANDOM WALKS FIRST-PASSAGE PROCESSES SUMMARY MATHEMATICAL APPENDIX Motor Proteins as Enzymes INTRODUCTION CATALYSIS ENZYMATIC PROCESSES SUMMARY MATHEMATICAL APPENDIX Theory for Motor Proteins: Continuum Ratchets INTRODUCTION CONTINUUM RATCHET POTENTIALS CRITICAL ANALYSIS SUMMARY Theory for Motor Proteins: Discrete-State Stochastic Models INTRODUCTION DISCRETE-STATE STOCHASTIC APPROACH CRITICAL ANALYSIS SUMMARY MATHEMATICAL APPENDIX Collective Properties of Motor Proteins COOPERATIVITY AND INTERACTIONS IN Motor Proteins DYNAMICS EXPERIMENTAL OBSERVATIONS THEORETICAL IDEAS SUMMARY Artificial Molecular Motors and Rotors INTRODUCTION BIOLOGICAL ARTIFICIAL MOLECULAR MotorS NON-BIOLOGICAL ARTIFICIAL MOLECULAR MotorS ARTIFICIAL MOLECULAR ROTORS SUMMARY Future Directions in Studies of Motor Proteins and Molecular Motors WHAT WE UNDERSTAND NOW ABOUT Motor Proteins AND MOLECULAR MotorS OPEN QUESTIONS AND PROBLEMS LOOKING INTO THE FUTURE Index

  • Motor Proteins and molecular Motors how to operate machines at the nanoscale
    Journal of Physics: Condensed Matter, 2013
    Co-Authors: Anatoly B. Kolomeisky
    Abstract:

    Several classes of biological molecules that transform chemical energy into mechanical work are known as Motor Proteins or molecular Motors. These nanometer-sized machines operate in noisy stochastic isothermal environments, strongly supporting fundamental cellular processes such as the transfer of genetic information, transport, organization and functioning. In the past two decades Motor Proteins have become a subject of intense research efforts, aimed at uncovering the fundamental principles and mechanisms of molecular Motor dynamics. In this review, we critically discuss recent progress in experimental and theoretical studies on Motor Proteins. Our focus is on analyzing fundamental concepts and ideas that have been utilized to explain the non-equilibrium nature and mechanisms of molecular Motors.