1
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Hatatani M, Yamamoto D, Shioi A. Surface-energy ratchet motor with geometrical symmetry driven by biased random walk. Sci Rep 2024; 14:16619. [PMID: 39025908 PMCID: PMC11258250 DOI: 10.1038/s41598-024-67383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
A geometrically symmetric gear with asymmetric surface wettability exhibits one-way spin on a vibrating water bed. On the side face of the gear, a parafilm was coated to create asymmetry in the surface energy. The gear shows fluctuations in both directions within a shorter timescale; however, for a longer timescale, the gear exhibits a one-way spin. This unique motion is generated by a stochastic process with a biased driving force produced by the interaction between the vibrating water surface and the side face of the gear. This new model resembles an active Brownian ratchet. Until now, most ratchet motors, which obtain regular motion from nonthermal fluctuations, utilize a geometrical ratchet structure. However, in this study, the surface energy forms a ratchet that rectifies the noisy motion.
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Affiliation(s)
- Miku Hatatani
- Department of Chemical Engineering and Materials Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0321, Japan
| | - Daigo Yamamoto
- Department of Chemical Engineering and Materials Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0321, Japan
| | - Akihisa Shioi
- Department of Chemical Engineering and Materials Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0321, Japan.
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2
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Watterson JG. The cluster model of energy transduction in biological systems. Biosystems 2024; 240:105213. [PMID: 38616011 DOI: 10.1016/j.biosystems.2024.105213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.
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3
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Marandi G, Hassanzadeh A. The rapid synthesis of 1,10-phenanthroline-5,6-diimine (Phendiimine) and its fascinating photo-stimulated behavior. Sci Rep 2024; 14:8464. [PMID: 38605215 PMCID: PMC11009400 DOI: 10.1038/s41598-024-59272-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/09/2024] [Indexed: 04/13/2024] Open
Abstract
Here, for the first time, we report synthesis of 1,10-phenanthroline-5,6-diimine (Phendiimine) based on an acid catalysed SN2 reaction of 1,10-phenanthroline-5,6-dione and 2-picolylamine in EtOH as a solvent. The synthesized Phendiimine molecule showed excellent photo-sensitivity against visible light, together with photoluminescence in both water and ethanol and also, it showed electrochemical activity with Fe electrode in ethanol and H2SO4 solution. Tauc plot also showed Phendiimine is a direct band-gap semiconductor. The hot-point probe test also showed that it is a n-type semiconductor. The UV-vis. absorption maximum shift in two solvents (water and ethanol) demonstrates the solvatochromism behavior of the molecule. The practical significance of this work and its guiding implication for future related research can be outlined as follows. Based on the results obtained, it appears that the Phendiimine molecule could revolutionize the medical field, potentially in the design of artificial eyes, increasing the yield of photovoltaic cells through enhanced heat transfer, improving computers and industrial photo-cooling systems, serving as photo-controller in place of piezoelectric devices, functioning as electronic opt couplers, controlling remote lasers, changing convection in photothermal heaters, designing miniaturized real photo-stimulated motors, creating photo or thermal switches through spin crossover complexes, developing electronic light-dependent resistance (LDR) devices, constructing X-ray and gamma-ray detectors, designing intelligent clothing, creating photo dynamic tumour therapy (PDT) complexes, singlet fission materials in solar cells and more.
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Affiliation(s)
- Ghasem Marandi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran.
| | - Ali Hassanzadeh
- Department of Physical Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
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4
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Zhang X, Wang S, Zhang J, Wang H. Memory induced-mechanism of noise attenuator of myosin V molecular motors. Biosystems 2024; 237:105139. [PMID: 38336223 DOI: 10.1016/j.biosystems.2024.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Depending on the chemical energy from ATP hydrolysis, myosin V can drive the multistep and continuous coupled cycling process to transport cellular cargo to targeted regions. However, it is still obscure how the molecular memory induced by the multistep coupled transported process could regulate the dynamic behavior of the motor state of myosin V. Here, we propose a novel non-Markovian polymorphic mechanochemical model to investigate the effect of the molecular memory on the mechanic of noise attenuation of myosin V system. We first define an effective transition rate for a multistep coupled reaction process which is the function of memory and system states to transform equivalently the non-Markovian process into the classical Markov process. By noise decomposition technology, it is observed that both the intrinsic and extrinsic noises of the ADP-myosin V bound state (AM ⋅ ADP) exhibit a monotonically decreasing trend with lengthening the molecular memory. Molecular memory as a regulation factor can amplify the contribution of intrinsic noise to the overall noise while reducing the influence of extrinsic noise on the AM ⋅ ADP. Moreover, the modulation of molecular memory could induce stochastic focusing. These results indicate that the role of molecular memory in the myosin V state transition can not only offer a handle to maintain the robustness of the motion system but also serve as a paradigm for studying more complex molecular motors.
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Affiliation(s)
- Xin Zhang
- School of Mathematics and Statistics, Hainan University, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, Haikou, 570228, Hainan, People's Republic of China
| | - Sizhe Wang
- The School of Mathematics, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jingwen Zhang
- School of Mathematics and Statistics, Hainan University, Haikou, 570228, Hainan, People's Republic of China; School of Cyberspace Security, Hainan University, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, Haikou, 570228, Hainan, People's Republic of China
| | - Haohua Wang
- School of Mathematics and Statistics, Hainan University, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, Haikou, 570228, Hainan, People's Republic of China.
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5
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Korosec CS, Unksov IN, Surendiran P, Lyttleton R, Curmi PMG, Angstmann CN, Eichhorn R, Linke H, Forde NR. Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle. Nat Commun 2024; 15:1511. [PMID: 38396042 PMCID: PMC10891099 DOI: 10.1038/s41467-024-45570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.
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Affiliation(s)
- Chapin S Korosec
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
- Department of Mathematics and Statistics, York University, Toronto, ON, M3J 1P3, Canada.
| | - Ivan N Unksov
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Pradheebha Surendiran
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Roman Lyttleton
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Christopher N Angstmann
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ralf Eichhorn
- Nordita, Royal Institute of Technology and Stockholm University, 106 91, Stockholm, Sweden
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden.
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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Singh H, Chenna A, Gangwar U, Dutta S, Kurur ND, Goel G, Haridas V. Bispidine as a promising scaffold for designing molecular machines. Org Biomol Chem 2023; 21:9054-9060. [PMID: 37937510 DOI: 10.1039/d3ob01406a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The development of artificial molecular machines is a challenging endeavor. Herein, we have synthesized a series of bispidine diamides D1-D6 that exhibit rotation reminiscent of a motor motion. Dynamic NMR, X-ray diffraction, quantum mechanical calculations, and molecular dynamics simulations provided insights into their rotational dynamics. All the diamides D1-D6 exhibited mutually independent rotation around the two bispidine arms. However, the rate of rotation and the presence or absence of directionality in amide bond rotation were found to depend on the solvent, temperature, and nature of substitution on the amide carbonyl. These engineered systems may aid in the development of biologically relevant synthetic molecular motors. Studies on homochiral and heterochiral bispidine-peptides revealed that the direction of rotation can be controlled by chirality and the nature of the amino acid.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India
| | - Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Souvik Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Narayanan D Kurur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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7
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Tomkiel AM, Majewski AD, Siergiejczyk L, Morzycki JW. Montmorillonite Catalyzed Synthesis of Novel Steroid Dimers. Molecules 2023; 28:7068. [PMID: 37894547 PMCID: PMC10609449 DOI: 10.3390/molecules28207068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The reactions of sterols (androst-5-en-3β-ol-17-one, diosgenin, and cholesterol) and their tosylates with hydroquinone aimed at the synthesis of O,O-1,4-phenylene-linked steroid dimers were studied. The reaction course strongly depended on the conditions used. The study has shown that the major reaction products are the elimination products and unusual steroid dimers resulting from the nucleophilic attack of the hydroquinone C2 carbon atom on the steroid C3 position, followed by an intramolecular addition to the C5-C6 double bond. A different reaction course was observed when montmorillonite K10 was used as a catalyst. The reaction of androst-5-en-3β-ol-17-one under the promotion of this catalyst afforded the O,O-1,4-phenylene-linked steroid dimer in addition to the disteroidal ether. The formation of the latter compound was suppressed by using 3-tosylate as a substrate instead of the free sterol. The reactions of androst-5-en-3β-ol-17-one tosylate and cholesteryl tosylate with hydroquinone catalyzed by montmorillonite K10 carried out under optimized conditions afforded the desired dimers in 31% and 67% yield, respectively.
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Affiliation(s)
- Aneta M. Tomkiel
- Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (A.D.M.); (L.S.)
| | - Adam D. Majewski
- Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (A.D.M.); (L.S.)
- Doctoral School of Exact and Natural Sciences, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland
| | - Leszek Siergiejczyk
- Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (A.D.M.); (L.S.)
| | - Jacek W. Morzycki
- Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland; (A.D.M.); (L.S.)
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8
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Nandel V, Scadden J, Baker MAB. Ion-Powered Rotary Motors: Where Did They Come from and Where They Are Going? Int J Mol Sci 2023; 24:10601. [PMID: 37445779 PMCID: PMC10341847 DOI: 10.3390/ijms241310601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Molecular motors are found in many living organisms. One such molecular machine, the ion-powered rotary motor (IRM), requires the movement of ions across a membrane against a concentration gradient to drive rotational movement. The bacterial flagellar motor (BFM) is an example of an IRM which relies on ion movement through the stator proteins to generate the rotation of the flagella. There are many ions which can be used by the BFM stators to power motility and different ions can be used by a single bacterium expressing multiple stator variants. The use of ancestral sequence reconstruction (ASR) and functional analysis of reconstructed stators shows promise for understanding how these proteins evolved and when the divergence in ion use may have occurred. In this review, we discuss extant BFM stators and the ions that power them as well as recent examples of the use of ASR to study ion-channel selectivity and how this might be applied to further study of the BFM stator complex.
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Affiliation(s)
| | | | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW 2033, Australia; (V.N.); (J.S.)
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9
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Singhania A, Kalita S, Chettri P, Ghosh S. Accounts of applied molecular rotors and rotary motors: recent advances. NANOSCALE ADVANCES 2023; 5:3177-3208. [PMID: 37325522 PMCID: PMC10262963 DOI: 10.1039/d3na00010a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Molecular machines are nanoscale devices capable of performing mechanical works at molecular level. These systems could be a single molecule or a collection of component molecules that interrelate with one another to produce nanomechanical movements and resulting performances. The design of the components of molecular machine with bioinspired traits results in various nanomechanical motions. Some known molecular machines are rotors, motors, nanocars, gears, elevators, and so on based on their nanomechanical motion. The conversion of these individual nanomechanical motions to collective motions via integration into suitable platforms yields impressive macroscopic output at varied sizes. Instead of limited experimental acquaintances, the researchers demonstrated several applications of molecular machines in chemical transformation, energy conversion, gas/liquid separation, biomedical use, and soft material fabrication. As a result, the development of new molecular machines and their applications has accelerated over the previous two decades. This review highlights the design principles and application scopes of several rotors and rotary motor systems because these machines are used in real applications. This review also offers a systematic and thorough overview of current advancements in rotary motors, providing in-depth knowledge and predicting future problems and goals in this area.
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Affiliation(s)
- Anup Singhania
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Sudeshna Kalita
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prerna Chettri
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Subrata Ghosh
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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10
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Liwo A, Pyrka M, Czaplewski C, Peng X, Niemi AJ. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules 2023; 13:941. [PMID: 37371521 DOI: 10.3390/biom13060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na+-ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Maciej Pyrka
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
- Department of Physics and Biophysics, University of Warmia and Mazury, ul. Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Antti J Niemi
- Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden
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Shivalkar S, Chowdhary P, Afshan T, Chaudhary S, Roy A, Samanta SK, Sahoo AK. Nanoengineering of biohybrid micro/nanobots for programmed biomedical applications. Colloids Surf B Biointerfaces 2023; 222:113054. [PMID: 36446238 DOI: 10.1016/j.colsurfb.2022.113054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022]
Abstract
Biohybrid micro/nanobots have emerged as an innovative resource to be employed in the biomedical field due to their biocompatible and biodegradable properties. These are tiny nanomaterial-based integrated structures engineered in a way that they can move autonomously and perform the programmed tasks efficiently even at hard-to-reach organ/tissues/cellular sites. The biohybrid micro/nanobots can either be cell/bacterial/enzyme-based or may mimic the properties of an active molecule. It holds the potential to change the landscape in various areas of biomedical including early diagnosis of disease, therapeutics, imaging, or precision surgery. The propulsion mechanism of the biohybrid micro/nanobots can be both fuel-based and fuel-free, but the most effective and easiest way to propel these micro/nanobots is via enzymes. Micro/nanobots possess the feature to adsorb/functionalize chemicals or drugs at their surfaces thus offering the scope of delivering drugs at the targeted locations. They also have shown immense potential in intracellular sensing of biomolecules and molecular events. Moreover, with recent progress in the material development and processing is required for enhanced activity and robustness the fabrication is done via various advanced techniques to avoid self-degradation and cause cellular toxicity during autonomous movement in biological medium. In this review, various approaches of design, architecture, and performance of such micro/nanobots have been illustrated along with their potential applications in controlled cargo release, therapeutics, intracellular sensing, and bioimaging. Furthermore, it is also foregrounding their advancement offering an insight into their future scopes, opportunities, and challenges involved in advanced biomedical applications.
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Affiliation(s)
- Saurabh Shivalkar
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India.
| | - Pallabi Chowdhary
- Department of Biotechnology, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Tayyaba Afshan
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India
| | - Shrutika Chaudhary
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Anwesha Roy
- Department of Biotechnology, Heritage Institute of Technology, Kolkata, West Bengal, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, UP, India.
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12
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Wagay SA, Khan L, Ali R. Recent Advancements in Ion-Pair Receptors. Chem Asian J 2023; 18:e202201080. [PMID: 36412231 DOI: 10.1002/asia.202201080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Over the past two decades, non-covalent chemistry has introduced various promising artificial receptors and revolutionized the host-guest chemistry. These versatile receptors have particularly been entertained in sensing and recognizing of diverse neutral molecules and/or ionic entities (e. g. anions, cations and ion-pair) of particular interest. Notably, supramolecular chemistry had given birth to a plethora of important molecules, explored in the chemical, biological, environmental, and pharmacological world to resolve the critical issues related to the human health while keeping environmental concerns in mind. Amongst the various types of supramolecular monotopic receptors (anions, cations, and neutral molecules), heteroditopic receptors (ion-pair receptors) consisting of distinct binding sites in one system for both cation and anion, have gained much interest from the scientific community in recent past because of their unique binding abilities. Interestingly, these promising artificial receptors have shown potential applications in sensing, recognition, transport and extraction processes besides their uses in salt/waste purification. Bearing the importance of these systems in mind, we intended to report the recent developments in ion-pair chemistry. Herein, we divided the whole document into three main sections; first one describes the introduction and history of the ion-pairs receptors. The second portion highlights the synthesis and applications of ion-pair receptors in sensing, recognition, molecular machines, photoswitching behaviour, extraction and transport properties, whereas the last part of this manuscript provides concluding remarks as well as future prospects of ion-pair receptors. We hope that this manuscript will be helpful to stimulating researchers around the globe to find out the hidden opportunities in this and related areas.
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Affiliation(s)
- Shafieq Ahmad Wagay
- Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Okhla, New Delhi, 110025, India
| | - Lubna Khan
- Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Okhla, New Delhi, 110025, India
| | - Rashid Ali
- Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Okhla, New Delhi, 110025, India
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13
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Cao XZ, Merlitz H, Wu CX, Forest MG. Screening confinement of entanglements: Role of a self-propelling end inducing ballistic chain reptation. Phys Rev E 2022; 106:L022501. [PMID: 36110008 DOI: 10.1103/physreve.106.l022501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Synthetic and natural nanomaterials with self-propelling mechanisms continue to be explored to boost chain mobility beyond normal reptation in the crowded environments of entangled chains. Here we employ scaling theory and numerical simulations to demonstrate that activating one chain end of a singular or isolated chain boosts entanglement-constrained chain reptation from the one-dimensional diffusive mobility as described by the de Gennes-Edwards-Doi model to ballistic motion along the entanglement tube contour. The active chain is effectively screened from the constraint of entanglements on length scales exceeding the tube size.
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Affiliation(s)
- Xue-Zheng Cao
- Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden, 01069 Dresden, Germany
| | - Chen-Xu Wu
- Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - M Gregory Forest
- Departments of Mathematics, Applied Physical Sciences, Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3250, USA
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14
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Photoresponsive Metal-Organic Frameworks as Adjustable Scaffolds in Reticular Chemistry. Int J Mol Sci 2022; 23:ijms23137121. [PMID: 35806126 PMCID: PMC9266399 DOI: 10.3390/ijms23137121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
The easy and remote switching of light makes this stimulus an ideal candidate for a large number of applications, among which the preparation of photoresponsive materials stands out. The interest of several scientists in this area in order to achieve improved functionalities has increase parallel to the growth of the structural complexity of these materials. Thus, metal-organic frameworks (MOFs) turned out to be ideal scaffolds for light-responsive ligands. This review is focused on the integration of photoresponsive organic ligands inside MOF crystalline arrays to prepare enhanced functional materials. Besides the summary of the preparation, properties and applications of these materials, an overview of the future outlook of this research area is provided.
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15
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Surendiran P, Meinecke CR, Salhotra A, Heldt G, Zhu J, Månsson A, Diez S, Reuter D, Kugler H, Linke H, Korten T. Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation. ACS NANOSCIENCE AU 2022; 2:396-403. [PMID: 36281252 PMCID: PMC9585575 DOI: 10.1021/acsnanoscienceau.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Information processing
by traditional, serial electronic processors
consumes an ever-increasing part of the global electricity supply.
An alternative, highly energy efficient, parallel computing paradigm
is network-based biocomputation (NBC). In NBC a given combinatorial
problem is encoded into a nanofabricated, modular network. Parallel
exploration of the network by a very large number of independent molecular-motor-propelled
protein filaments solves the encoded problem. Here we demonstrate
a significant scale-up of this technology by solving four instances
of Exact Cover, a nondeterministic polynomial time (NP) complete problem
with applications in resource scheduling. The difficulty of the largest
instances solved here is 128 times greater in comparison to the current
state of the art for NBC.
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Affiliation(s)
| | | | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Georg Heldt
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Jingyuan Zhu
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden D-01307, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden D-01307, Germany
| | - Danny Reuter
- Center for Microtechnologies, Technische Universität Chemnitz, Chemnitz D-09126, Germany
- Fraunhofer Institute for Electronic Nano Systems ENAS, Chemnitz, D-09126, Germany
| | - Hillel Kugler
- Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Till Korten
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
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16
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Optimizing Efficiency and Motility of a Polyvalent Molecular Motor. MICROMACHINES 2022; 13:mi13060914. [PMID: 35744528 PMCID: PMC9228586 DOI: 10.3390/mi13060914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
Molecular motors play a vital role in the transport of material within the cell. A family of motors of growing interest are burnt bridge ratchets (BBRs). BBRs rectify spatial fluctuations into directed motion by creating and destroying motor-substrate bonds. It has been shown that the motility of a BBR can be optimized as a function of the system parameters. However, the amount of energy input required to generate such motion and the resulting efficiency has been less well characterized. Here, using a deterministic model, we calculate the efficiency of a particular type of BBR, namely a polyvalent hub interacting with a surface of substrate. We find that there is an optimal burn rate and substrate concentration that leads to optimal efficiency. Additionally, the substrate turnover rate has important implications on motor efficiency. We also consider the effects of force-dependent unbinding on the efficiency and find that under certain conditions the motor works more efficiently when bond breaking is included. Our results provide guidance for how to optimize the efficiency of BBRs.
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17
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Shi D, An K, Zhang H, Xu P, Bai C. Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines. ENTROPY 2022; 24:e24050620. [PMID: 35626506 PMCID: PMC9140642 DOI: 10.3390/e24050620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 12/14/2022]
Abstract
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Ke An
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Honghui Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
| | - Peiyi Xu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- Correspondence:
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18
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Falahati M, Sharifi M, Hagen TLMT. Explaining chemical clues of metal organic framework-nanozyme nano-/micro-motors in targeted treatment of cancers: benchmarks and challenges. J Nanobiotechnology 2022; 20:153. [PMID: 35331244 PMCID: PMC8943504 DOI: 10.1186/s12951-022-01375-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/12/2022] [Indexed: 02/07/2023] Open
Abstract
Nowadays, nano-/micro-motors are considered as powerful tools in different areas ranging from cleaning all types of contaminants, to development of Targeted drug delivery systems and diagnostic activities. Therefore, the development and application of nano-/micro-motors based on metal-organic frameworks with nanozyme activity (abbreviated as: MOF-NZs) in biomedical activities have received much interest recently. Therefore, after investigating the catalytic properties and applications of MOF-NZs in the treatment of cancer, this study intends to point out their key role in the production of biocompatible nano-/micro-motors. Since reducing the toxicity of MOF-NZ nano-/micro-motors can pave the way for medical activities, this article examines the methods of making biocompatible nanomotors to address the benefits and drawbacks of the required propellants. In the following, an analysis of the amplified directional motion of MOF-NZ nano-/micro-motors under physiological conditions is presented, which can improve the motor behaviors in the propulsion function, conductivity, targeting, drug release, and possible elimination. Meanwhile, by explaining the use of MOF-NZ nano-/micro-motors in the treatment of cancer through the possible synergy of nanomotors with different therapies, it was revealed that MOF-NZ nano-/micro-motors can be effective in the treatment of cancer. Ultimately, by analyzing the potential challenges of MOF-NZ nano-/micro-motors in the treatment of cancers, we hope to encourage researchers to develop MOF-NZs-based nanomotors, in addition to opening up new ideas to address ongoing problems.
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Affiliation(s)
- Mojtaba Falahati
- Laboratory Experimental Oncology, Department of Pathology, Erasmus MC, 3015GD, Rotterdam, The Netherlands.
| | - Majid Sharifi
- Student Research Committee, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.
- Depatment of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.
| | - Timo L M Ten Hagen
- Laboratory Experimental Oncology, Department of Pathology, Erasmus MC, 3015GD, Rotterdam, The Netherlands.
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19
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Jeong Y, Jin S, Palanikumar L, Choi H, Shin E, Go EM, Keum C, Bang S, Kim D, Lee S, Kim M, Kim H, Lee KH, Jana B, Park MH, Kwak SK, Kim C, Ryu JH. Stimuli-Responsive Adaptive Nanotoxin to Directly Penetrate the Cellular Membrane by Molecular Folding and Unfolding. J Am Chem Soc 2022; 144:5503-5516. [PMID: 35235326 DOI: 10.1021/jacs.2c00084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological nanomachines, including proteins and nucleic acids whose function is activated by conformational changes, are involved in every biological process, in which their dynamic and responsive behaviors are controlled by supramolecular recognition. The development of artificial nanomachines that mimic the biological functions for potential application as therapeutics is emerging; however, it is still limited to the lower hierarchical level of the molecular components. In this work, we report a synthetic machinery nanostructure in which actuatable molecular components are integrated into a hierarchical nanomaterial in response to external stimuli to regulate biological functions. Two nanometers core-sized gold nanoparticles are covered with ligand layers as actuatable components, whose folding/unfolding motional response to the cellular environment enables the direct penetration of the nanoparticles across the cellular membrane to disrupt intracellular organelles. Furthermore, the pH-responsive conformational movements of the molecular components can induce the apoptosis of cancer cells. This strategy based on the mechanical motion of molecular components on a hierarchical nanocluster would be useful to design biomimetic nanotoxins.
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Affiliation(s)
- Youngdo Jeong
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Soyeong Jin
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - L Palanikumar
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Huyeon Choi
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eunhye Shin
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Eun Min Go
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Changjoon Keum
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seunghwan Bang
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Dongkap Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seungho Lee
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Minsoo Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hojun Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kwan Hyi Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Batakrishna Jana
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Myoung-Hwan Park
- Department of Chemistry & Life Science, Sahmyook University, Seoul 01795, Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Chaekyu Kim
- Fusion Biotechnology, Inc., Ulsan 44919, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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20
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Stähler C, Grunenberg L, Terban MW, Browne WR, Doellerer D, Kathan M, Etter M, Lotsch BV, Feringa BL, Krause S. Light-Driven Molecular Motors Embedded in Covalent Organic Frameworks. Chem Sci 2022; 13:8253-8264. [PMID: 35919721 PMCID: PMC9297439 DOI: 10.1039/d2sc02282f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/21/2022] Open
Abstract
The incorporation of molecular machines into the backbone of porous framework structures will facilitate nano actuation, enhanced molecular transport, and other out-of-equilibrium host-guest phenomena in well-defined 3D solid materials. In...
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Affiliation(s)
- Cosima Stähler
- Stratingh Institute for Chemistry, Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Lars Grunenberg
- Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU) Butenandtstr. 5-13 81377 Munich Germany
| | - Maxwell W Terban
- Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Daniel Doellerer
- Stratingh Institute for Chemistry, Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Michael Kathan
- Stratingh Institute for Chemistry, Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY) Notkestr. 85 22607 Hamburg Germany
| | - Bettina V Lotsch
- Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU) Butenandtstr. 5-13 81377 Munich Germany
- E-conversion Lichtenbergstrasse 4a 85748 Garching Germany
| | - Ben L Feringa
- Stratingh Institute for Chemistry, Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Simon Krause
- Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany
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21
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Paneru G, Park JT, Pak HK. Transport and Diffusion Enhancement in Experimentally Realized Non-Gaussian Correlated Ratchets. J Phys Chem Lett 2021; 12:11078-11084. [PMID: 34748337 DOI: 10.1021/acs.jpclett.1c03037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Living cells are known to generate non-Gaussian active fluctuations significantly larger than thermal fluctuations owing to various active processes. Understanding the effect of these active fluctuations on various physicochemical processes, such as the transport of molecular motors, is a fundamental problem in nonequilibrium physics. Therefore, we experimentally and numerically studied an active Brownian ratchet comprising a colloidal particle in an optically generated asymmetric periodic potential driven by non-Gaussian noise having finite-amplitude active bursts, each arriving at random and decaying exponentially. We find that the particle velocity is maximum for relatively sparse bursts with finite correlation time and non-Gaussian distribution. These occasional kicks, which produce Brownian yet non-Gaussian diffusion, are more efficient for transport and diffusion enhancement of the particle than the incessant kicks of active Ornstein-Uhlenbeck noise.
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Affiliation(s)
- Govind Paneru
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jin Tae Park
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Hyuk Kyu Pak
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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22
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Maloul S, van den Borg M, Müller C, Zedler L, Mengele AK, Gaissmaier D, Jacob T, Rau S, Dietzek-Ivanšić B, Streb C. Multifunctional Polyoxometalate Platforms for Supramolecular Light-Driven Hydrogen Evolution*. Chemistry 2021; 27:16846-16852. [PMID: 34719797 PMCID: PMC9299148 DOI: 10.1002/chem.202103817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 11/17/2022]
Abstract
Multifunctional supramolecular systems are a central research topic in light‐driven solar energy conversion. Here, we report a polyoxometalate (POM)‐based supramolecular dyad, where two platinum‐complex hydrogen evolution catalysts are covalently anchored to an Anderson polyoxomolybdate anion. Supramolecular electrostatic coupling of the system to an iridium photosensitizer enables visible light‐driven hydrogen evolution. Combined theory and experiment demonstrate the multifunctionality of the POM, which acts as photosensitizer/catalyst‐binding‐site[1] and facilitates light‐induced charge‐transfer and catalytic turnover. Chemical modification of the Pt‐catalyst site leads to increased hydrogen evolution reactivity. Mechanistic studies shed light on the role of the individual components and provide a molecular understanding of the interactions which govern stability and reactivity. The system could serve as a blueprint for multifunctional polyoxometalates in energy conversion and storage.
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Affiliation(s)
- Salam Maloul
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Matthias van den Borg
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081, Ulm, Germany
| | - Carolin Müller
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technologies (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Linda Zedler
- Leibniz Institute of Photonic Technologies (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Alexander K Mengele
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Daniel Gaissmaier
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081, Ulm, Germany.,Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtzstr. 11, 89081, Ulm, Germany.,Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081, Ulm, Germany.,Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtzstr. 11, 89081, Ulm, Germany.,Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Karlsruhe, Germany
| | - Sven Rau
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Benjamin Dietzek-Ivanšić
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Leibniz Institute of Photonic Technologies (IPHT), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Carsten Streb
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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23
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Hayashi K, Niwa S. Japan-US symposium on cytoskeletal motor proteins and their associated proteins. Biophys Physicobiol 2021; 18:241-243. [PMID: 34745808 PMCID: PMC8550873 DOI: 10.2142/biophysico.bppb-v18.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Kumiko Hayashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, Miyagi 980-0845, Japan
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
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24
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Paolino M, Giovannini T, Manathunga M, Latterini L, Zampini G, Pierron R, Léonard J, Fusi S, Giorgi G, Giuliani G, Cappelli A, Cappelli C, Olivucci M. On the Transition from a Biomimetic Molecular Switch to a Rotary Molecular Motor. J Phys Chem Lett 2021; 12:3875-3884. [PMID: 33856801 DOI: 10.1021/acs.jpclett.1c00526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The experimental investigation of the unidirectional motion characterizing the photoisomerization of single-molecule rotary motors requires accessible lab prototypes featuring an electronic circular dichroism (ECD) signal that is sensitive to the geometrical and electronic changes occurring during an ultrafast reactive process. Here we report a combined experimental/computational study of a candidate obtained via the asymmetrization of a light-driven biomimetic molecular switch. We show that the achieved motor has an ECD band that is remarkably sensitive to the isomerization motion, and it is therefore suitable for time-resolved ECD studies. However, we also find that, unexpectedly, the synthesized motor isomerizes on a time scale longer than the subpicosecond time measured for the achiral parent, a result that points to alternative candidates conserving a high reaction speed.
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Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | | | - Madushanka Manathunga
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403-0001, United States
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Giulia Zampini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Robin Pierron
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
| | - Stefania Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403-0001, United States
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25
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Feng Y, Ovalle M, Seale JSW, Lee CK, Kim DJ, Astumian RD, Stoddart JF. Molecular Pumps and Motors. J Am Chem Soc 2021; 143:5569-5591. [PMID: 33830744 DOI: 10.1021/jacs.0c13388] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pumps and motors are essential components of the world as we know it. From the complex proteins that sustain our cells, to the mechanical marvels that power industries, much we take for granted is only possible because of pumps and motors. Although molecular pumps and motors have supported life for eons, it is only recently that chemists have made progress toward designing and building artificial forms of the microscopic machinery present in nature. The advent of artificial molecular machines has granted scientists an unprecedented level of control over the relative motion of components of molecules through the development of kinetically controlled, away-from-thermodynamic equilibrium chemistry. We outline the history of pumps and motors, focusing specifically on the innovations that enable the design and synthesis of the artificial molecular machines central to this Perspective. A key insight connecting biomolecular and artificial molecular machines is that the physical motions by which these machines carry out their function are unambiguously in mechanical equilibrium at every instant. The operation of molecular motors and pumps can be described by trajectory thermodynamics, a theory based on the work of Onsager, which is grounded on the firm foundation of the principle of microscopic reversibility. Free energy derived from thermodynamically non-equilibrium reactions kinetically favors some reaction pathways over others. By designing molecules with kinetic asymmetry, one can engineer potential landscapes to harness external energy to drive the formation and maintenance of geometries of component parts of molecules away-from-equilibrium, that would be impossible to achieve by standard synthetic approaches.
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Affiliation(s)
- Yuanning Feng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Ovalle
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - James S W Seale
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Christopher K Lee
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dong Jun Kim
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - R Dean Astumian
- Department of Physics, University of Maine, Orono, Maine 04469, United States
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.,Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
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Fu H, Chipot C, Cai W, Shao X. Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions. J Phys Chem Lett 2021; 12:613-619. [PMID: 33382629 DOI: 10.1021/acs.jpclett.0c03444] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To understand how different external stimuli affect the cooperative motions in a molecular machine consisting of multiple components, we have investigated at the atomic level the effects of pH, solvent, and ionic strength on the mechanism underlying the ring-through-ring movement in a saturated [3]rotaxane. Our results indicate that different external stimuli regulate the stable states, the shuttling rate, and the mechanism that governs the ring-through-ring motion by controlling the cooperative movement of the components and triggering a gamut of responses, thereby opening to a vast number of potential applications, such as quaternary logical calculations. The present work cogently demonstrates that with existing nanomachines possessing a simple topology, but using different external stimuli-an approach coined multidimensional regulation-challenging tasks requiring precise control of the molecular motions at play can be achieved, and our methodology is particularly germane for de novo design of intelligent molecular machines.
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Affiliation(s)
- Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR No. 7019, Université de Lorraine, BP 70239, F-54506 Vandœuvre-lès-Nancy, France
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
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Ganie AA, Ismail TM, Sajith PK, Dar AA. Validation of the supramolecular synthon preference through DFT and physicochemical property investigations of pyridyl salts of organo-sulfonates. NEW J CHEM 2021. [DOI: 10.1039/d0nj05485b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding of the supramolecular synthon competition is sparse and the synthon hierarchy studies are limited. Herein, we validate the synthon preferences in multi-functional organic precursor through DFT and crystallographic studies.
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Affiliation(s)
- Arshid A. Ganie
- Department of Chemistry
- Inorganic Section
- University of Kashmir
- Hazratbal
- India
| | | | - P. K. Sajith
- Department of Chemistry
- Farook College
- Kozhikode
- India
| | - Aijaz A. Dar
- Department of Chemistry
- Inorganic Section
- University of Kashmir
- Hazratbal
- India
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29
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Linke H, Höcker B, Furuta K, Forde NR, Curmi PMG. Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev 2020; 12:1041-1054. [PMID: 32651904 PMCID: PMC7429643 DOI: 10.1007/s12551-020-00717-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.
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Affiliation(s)
- Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE 22100, Lund, Sweden
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.
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Ruyonga MR, Mendoza O, Browne M, Samoshin VV. Exploration of
trans
‐2‐(azaarylsulfanyl)‐cyclohexanols as potential pH‐triggered conformational switches. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mulinde R. Ruyonga
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Oscar Mendoza
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Michael Browne
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
| | - Vyacheslav V. Samoshin
- Department of Chemistry, College of the Pacific University of the Pacific Stockton CA USA
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Kabir AMR, Inoue D, Kakugo A. Molecular swarm robots: recent progress and future challenges. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2020; 21:323-332. [PMID: 32939158 PMCID: PMC7476543 DOI: 10.1080/14686996.2020.1761761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Recent advancements in molecular robotics have been greatly contributed by the progress in various fields of science and technology, particularly in supramolecular chemistry, bio- and nanotechnology, and informatics. Yet one of the biggest challenges in molecular robotics has been controlling a large number of robots at a time and employing the robots for any specific task as flocks in order to harness emergent functions. Swarming of molecular robots has emerged as a new paradigm with potentials to overcome this hurdle in molecular robotics. In this review article, we comprehensively discuss the latest developments in swarm molecular robotics, particularly emphasizing the effective utilization of bio- and nanotechnology in swarming of molecular robots. Importance of tuning the mutual interaction among the molecular robots in regulation of their swarming is introduced. Successful utilization of DNA, photoresponsive molecules, and natural molecular machines in swarming of molecular robots to provide them with processing, sensing, and actuating ability is highlighted. The potentials of molecular swarm robots for practical applications by means of their ability to participate in logical operations and molecular computations are also discussed. Prospects of the molecular swarm robots in utilizing the emergent functions through swarming are also emphasized together with their future perspectives.
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Affiliation(s)
| | - Daisuke Inoue
- Faculty of Design, Department of Human Science, Kyushu University, Fukuoka, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
- CONTACT Akira Kakugo Hokkaido University, Sapporo shi, Kita ku, Kita 10, Nishi 8, Science building-7, Room-215, Sapporo060-0810, Japan
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