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Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms...
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Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 22984

Special Issue Editors

Prof. Dr. Massimo Reconditi

E-Mail Website
Guest Editor
Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
Interests: muscle physiology; mathematical modelling of muscle contraction; mechanics and structure of molecular motors
Special Issues, Collections and Topics in MDPI journals
Dr. Marco Capitanio

E-Mail Website
Guest Editor
1. Department of Physics and Astronomy, Università degli Studi di Firenze, 50019 Florence, Italy
2. LENS (European Laboratory for Non-linear Spectroscopy), 50019 Sesto Fiorentino, Italy
Interests: single molecule biophysics; molecular motors; mechanobiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular motors, or motor proteins, transform chemical energy into mechanical output. Because of their many fundamental biological functions, molecular motors are ubiquitous in living cells: to cover but a few of these functions, they are responsible for cell movement and division, driving intracellular trafficking inside the cell, and may work cooperatively to produce macroscopic outputs such as in the case of muscle contraction.

In the last quarter of a century, different techniques have been developed to allow the biophysical properties of the molecular motors to be studied at the level of the single molecule, both in vitro and in situ. These properties must be integrated into studies that correlate them with their role in cell physiology. Despite the significant advances which have occurred in recent years, the fundamental mechanisms of their functioning are still not fully understood.

The aim of this Special Issue is to bring together reviews and original papers on the structure and function of the different classes of molecular motors, and on their action inside the cell.

We believe that there would be great interest in such topics as the cooperative action of molecular motors, the regulation of their activity, and mutations or post-translational modifications that may lead to pathological disfunctions. From an experimental point of view, novel or refined techniques and analyses that allow uncovering new mechanisms of motor protein function will be of particular interest.

Prof. Dr. Massimo Reconditi
Dr. Marco Capitanio
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Related Special Issue

Published Papers (7 papers)

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Editorial

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3 pages, 178 KiB  
Editorial
Editorial to the Special Issue “Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo”
by Marco Capitanio and Massimo Reconditi
Int. J. Mol. Sci. 2022, 23(12), 6605; https://doi.org/10.3390/ijms23126605 - 14 Jun 2022
Viewed by 1603
Abstract
The Molecular motors or motor proteins are able to generate force and do mechanical work that is used to displace a load or produce relative movements between molecules or macromolecular assembles [...] Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)

Research

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19 pages, 1883 KiB  
Article
The Synergic Role of Actomyosin Architecture and Biased Detachment in Muscle Energetics: Insights in Cross Bridge Mechanism beyond the Lever-Arm Swing
by Lorenzo Marcucci, Hiroki Fukunaga, Toshio Yanagida and Mitsuhiro Iwaki
Int. J. Mol. Sci. 2021, 22(13), 7037; https://doi.org/10.3390/ijms22137037 - 29 Jun 2021
Cited by 5 | Viewed by 2227
Abstract
Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sliding velocity based on DNA-origami [...] Read more.
Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and Monte Carlo simulations based on a model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate less considered components in the chemo-mechanical energy transduction in muscle. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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10 pages, 2498 KiB  
Article
Biased Brownian Motion of KIF1A and the Role of Tubulin’s C-Terminal Tail Studied by Molecular Dynamics Simulation
by Yukinobu Mizuhara and Mitsunori Takano
Int. J. Mol. Sci. 2021, 22(4), 1547; https://doi.org/10.3390/ijms22041547 - 4 Feb 2021
Cited by 3 | Viewed by 2834
Abstract
KIF1A is a kinesin family protein that moves over a long distance along the microtubule (MT) to transport synaptic vesicle precursors in neurons. A single KIF1A molecule can move toward the plus-end of MT in the monomeric form, exhibiting the characteristics of biased [...] Read more.
KIF1A is a kinesin family protein that moves over a long distance along the microtubule (MT) to transport synaptic vesicle precursors in neurons. A single KIF1A molecule can move toward the plus-end of MT in the monomeric form, exhibiting the characteristics of biased Brownian motion. However, how the bias is generated in the Brownian motion of KIF1A has not yet been firmly established. To elucidate this, we conducted a set of molecular dynamics simulations and observed the binding of KIF1A to MT. We found that KIF1A exhibits biased Brownian motion along MT as it binds to MT. Furthermore, we show that the bias toward the plus-end is generated by the ratchet-like energy landscape for the KIF1A-MT interaction, in which the electrostatic interaction and the negatively-charged C-terminal tail (CTT) of tubulin play an essential role. The relevance to the post-translational modifications of CTT is also discussed. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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14 pages, 1653 KiB  
Article
A Myosin II-Based Nanomachine Devised for the Study of Ca2+-Dependent Mechanisms of Muscle Regulation
by Irene Pertici, Giulio Bianchi, Lorenzo Bongini, Vincenzo Lombardi and Pasquale Bianco
Int. J. Mol. Sci. 2020, 21(19), 7372; https://doi.org/10.3390/ijms21197372 - 6 Oct 2020
Cited by 10 | Viewed by 2742
Abstract
The emergent properties of the array arrangement of the molecular motor myosin II in the sarcomere of the striated muscle, the generation of steady force and shortening, can be studied in vitro with a synthetic nanomachine made of an ensemble of eight heavy-meromyosin [...] Read more.
The emergent properties of the array arrangement of the molecular motor myosin II in the sarcomere of the striated muscle, the generation of steady force and shortening, can be studied in vitro with a synthetic nanomachine made of an ensemble of eight heavy-meromyosin (HMM) fragments of myosin from rabbit psoas muscle, carried on a piezoelectric nanopositioner and brought to interact with a properly oriented actin filament attached via gelsolin (a Ca2+-regulated actin binding protein) to a bead trapped by dual laser optical tweezers. However, the application of the original version of the nanomachine to investigate the Ca2+-dependent regulation mechanisms of the other sarcomeric (regulatory or cytoskeleton) proteins, adding them one at a time, was prevented by the impossibility to preserve [Ca2+] as a free parameter. Here, the nanomachine is implemented by assembling the bead-attached actin filament with the Ca2+-insensitive gelsolin fragment TL40. The performance of the nanomachine is determined both in the absence and in the presence of Ca2+ (0.1 mM, the concentration required for actin attachment to the bead with gelsolin). The nanomachine exhibits a maximum power output of 5.4 aW, independently of [Ca2+], opening the possibility for future studies of the Ca2+-dependent function/dysfunction of regulatory and cytoskeletal proteins. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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Review

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16 pages, 515 KiB  
Review
Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability
by Aaron Morgan, Sarah LeGresley and Christopher Fischer
Int. J. Mol. Sci. 2021, 22(1), 76; https://doi.org/10.3390/ijms22010076 - 23 Dec 2020
Cited by 8 | Viewed by 3516
Abstract
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active [...] Read more.
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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18 pages, 3416 KiB  
Review
How Kinesin-1 Utilize the Energy of Nucleotide: The Conformational Changes and Mechanochemical Coupling in the Unidirectional Motion of Kinesin-1
by Jingyu Qin, Hui Zhang, Yizhao Geng and Qing Ji
Int. J. Mol. Sci. 2020, 21(18), 6977; https://doi.org/10.3390/ijms21186977 - 22 Sep 2020
Cited by 20 | Viewed by 5075
Abstract
Kinesin-1 is a typical motile molecular motor and the founding member of the kinesin family. The most significant feature in the unidirectional motion of kinesin-1 is its processivity. To realize the fast and processive movement on the microtubule lattice, kinesin-1 efficiently transforms the [...] Read more.
Kinesin-1 is a typical motile molecular motor and the founding member of the kinesin family. The most significant feature in the unidirectional motion of kinesin-1 is its processivity. To realize the fast and processive movement on the microtubule lattice, kinesin-1 efficiently transforms the chemical energy of nucleotide binding and hydrolysis to the energy of mechanical movement. The chemical and mechanical cycle of kinesin-1 are coupled to avoid futile nucleotide hydrolysis. In this paper, the research on the mechanical pathway of energy transition and the regulating mechanism of the mechanochemical cycle of kinesin-1 is reviewed. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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Other

21 pages, 2958 KiB  
Hypothesis
Hypothesis: Single Actomyosin Properties Account for Ensemble Behavior in Active Muscle Shortening and Isometric Contraction
by Alf Månsson
Int. J. Mol. Sci. 2020, 21(21), 8399; https://doi.org/10.3390/ijms21218399 - 9 Nov 2020
Cited by 12 | Viewed by 3791
Abstract
Muscle contraction results from cyclic interactions between myosin II motors and actin with two sets of proteins organized in overlapping thick and thin filaments, respectively, in a nearly crystalline lattice in a muscle sarcomere. However, a sarcomere contains a huge number of other [...] Read more.
Muscle contraction results from cyclic interactions between myosin II motors and actin with two sets of proteins organized in overlapping thick and thin filaments, respectively, in a nearly crystalline lattice in a muscle sarcomere. However, a sarcomere contains a huge number of other proteins, some with important roles in muscle contraction. In particular, these include thin filament proteins, troponin and tropomyosin; thick filament proteins, myosin binding protein C; and the elastic protein, titin, that connects the thin and thick filaments. Furthermore, the order and 3D organization of the myofilament lattice may be important per se for contractile function. It is possible to model muscle contraction based on actin and myosin alone with properties derived in studies using single molecules and biochemical solution kinetics. It is also possible to reproduce several features of muscle contraction in experiments using only isolated actin and myosin, arguing against the importance of order and accessory proteins. Therefore, in this paper, it is hypothesized that “single molecule actomyosin properties account for the contractile properties of a half sarcomere during shortening and isometric contraction at almost saturating Ca concentrations”. In this paper, existing evidence for and against this hypothesis is reviewed and new modeling results to support the arguments are presented. Finally, further experimental tests are proposed, which if they corroborate, at least approximately, the hypothesis, should significantly benefit future effective analysis of a range of experimental studies, as well as drug discovery efforts. Full article
(This article belongs to the Special Issue Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo)
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