1
|
Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [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: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
Collapse
Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
| |
Collapse
|
2
|
The Rationale for Using Neridronate in Musculoskeletal Disorders: From Metabolic Bone Diseases to Musculoskeletal Pain. Int J Mol Sci 2022; 23:ijms23136921. [PMID: 35805927 PMCID: PMC9267106 DOI: 10.3390/ijms23136921] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Neridronate or ((6-amino-1-hydroxy-1-phosphonohexyl) phosphonic acid) is an amino-bisphosphonate (BP) synthetized in Italy in 1986. Bisphosphonates are molecules with a P-C-P bond in their structure that allows strong and selectively binding to hydroxyapatite (HAP) as well as osteoclasts inhibition through different mechanisms of action. Neridronate was initially used to treat Paget disease of the bone, demonstrating effectiveness in reducing bone turnover markers as well as pain. The interesting molecular properties of neridronate foster its wide use in several other conditions, such as osteogenesis imperfecta, and osteoporosis. Thanks to the unique safety and efficacy profile, neridronate has been used in secondary osteoporosis due to genetic, rheumatic, and oncological diseases, including in pediatric patients. In the last decade, this drug has also been studied in chronic musculoskeletal pain conditions, such as algodystrophy, demonstrating effectiveness in improving extraskeletal outcomes. This review highlights historical and clinical insights about the use of neridronate for metabolic bone disorders and musculoskeletal pain conditions.
Collapse
|
3
|
Zhu Y, Qiu X, Chen X, Huang M, Li Y. Single gold nanowire-based nanosensor for adenosine triphosphate sensing by using in-situ surface-enhanced Raman scattering technique. Talanta 2022; 249:123675. [PMID: 35716474 DOI: 10.1016/j.talanta.2022.123675] [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: 04/23/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 10/31/2022]
Abstract
Development of new hot spots for surface enhanced Raman scattering (SERS) technique is of great significance recently. Herein, we developed a single Au nanowire (NW)-based nanosensor for adenosine triphosphate (ATP) sensing by using in-situ SERS technique. Single Au NWs, fabricated by laser-assisted pulling method and hydrofluoric acid (HF) etching process, were linked with single-stranded HS-terminated DNA. After that, gold-silver bimetallic nanoparticles (Au/Ag NPs), attached with thiol-containing Raman dyes and ATP aptamer, were immobilized on DNA-modified single AuNW due to the designed affinity between ATP aptamer and single-stranded DNA. This single AuNW-based device exhibited strong SERS signals. In the presence of adenosine triphosphate (ATP), due to the strong specific affinity between the aptamer and the target, the Au/Ag NPs will be separated from the AuNW, resulting in the obvious decrease of the Raman signals, which can be used for ATP sensing with high sensitivity, selectivity and stability. This nanosensor can be used as an ideal platform for real applications, especially at some confined-space samples, such as trace detection, single cell and in vivo analysis.
Collapse
Affiliation(s)
- Yanyan Zhu
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xia Qiu
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xiaohu Chen
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Mimi Huang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China.
| |
Collapse
|
4
|
Kurisaki I, Tanaka S. Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras-GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage. Phys Chem Chem Phys 2021; 23:26151-26164. [PMID: 34797363 DOI: 10.1039/d1cp04061h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ATPase and GTPase have been widely found as chemical energy-mechanical work transducers, whereas the physicochemical mechanisms are not satisfactorily understood. We addressed the problem by examining John Ross' conjecture that repulsive Coulomb interaction between ADP/GDP and inorganic phosphate (Pi) does the mechanical work upon the system. We effectively simulated the consequence of a GTP hydrolysis reaction in a complex system of Rat sarcoma (Ras) and GTPase activation protein (GAP) in the framework of classical molecular dynamics by switching force field parameters between the reactant and product systems. We then observed a ca. 5 kcal mol-1 increase of potential energy about the phosphate-binding loop (P-loop) in the Ras protein, indicating that the mechanical work generated via the GTP hydrolysis is converted into the local interaction energy and stored in the P-loop. Interestingly, this local energy storage in the P-loop depends on neither impulsive nor consecutive collisions of GDP and Pi with the P-loop. Instead, GTP-GDP conversion itself does work on the Ras system, elevating the potential energy. These observations encourage us to challenge a conjecture previously given by Ross. We assert that triphosphate nucleotide hydrolyses do mechanical work by producing emergent steric interaction accompanied by relaxation, namely, a shift of the biomolecular system to the non-equilibrium state on the reshaped potential energy landscape. Recalling the universality of the P-loop motif among GTPases and ATPases, the observations that we obtained through this study would progress the physicochemical understanding of the operating principles of GTP/ATP hydrolysis-driven biological nano-machines.
Collapse
Affiliation(s)
- Ikuo Kurisaki
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| |
Collapse
|
5
|
Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method. Molecules 2018; 23:molecules23102652. [PMID: 30332773 PMCID: PMC6222333 DOI: 10.3390/molecules23102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022] Open
Abstract
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
Collapse
Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| |
Collapse
|
6
|
Pan TCF, Applebaum SL, Frieder CA, Manahan DT. Biochemical bases of growth variation during development: a study of protein turnover in pedigreed families of bivalve larvae ( Crassostrea gigas). ACTA ACUST UNITED AC 2018; 221:jeb.171967. [PMID: 29615524 DOI: 10.1242/jeb.171967] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/22/2018] [Indexed: 01/08/2023]
Abstract
Animal size is a highly variable trait regulated by complex interactions between biological and environmental processes. Despite the importance of understanding the mechanistic bases of growth, predicting size variation in early stages of development remains challenging. Pedigreed lines of the Pacific oyster (Crassostrea gigas) were crossed to produce contrasting growth phenotypes to analyze the metabolic bases of growth variation in larval stages. Under controlled environmental conditions, substantial growth variation of up to 430% in shell length occurred among 12 larval families. Protein was the major biochemical constituent in larvae, with an average protein-to-lipid content ratio of 2.8. On average, 86% of protein synthesized was turned over (i.e. only 14% retained as protein accreted), with a regulatory shift in depositional efficiency resulting in increased protein accretion during later larval growth. Variation in protein depositional efficiency among families did not explain the range in larval growth rates. Instead, changes in protein synthesis rates predicted 72% of growth variation. High rates of protein synthesis to support faster growth, in turn, necessitated greater allocation of the total ATP pool to protein synthesis. An ATP allocation model is presented for larvae of C. gigas that includes the major components (82%) of energy demand: protein synthesis (45%), ion pump activity (20%), shell formation (14%) and protein degradation (3%). The metabolic trade-offs between faster growth and the need for higher ATP allocation to protein synthesis could be a major determinant of fitness for larvae of different genotypes responding to the stress of environmental change.
Collapse
Affiliation(s)
- T-C Francis Pan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Scott L Applebaum
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Christina A Frieder
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Donal T Manahan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| |
Collapse
|
7
|
Wang Y, Fu L, Qi H, Chen SW, Li Y. Bioinspired Synthesis of Nitriles from Primary Amides via Zinc/Anhydride Catalysis. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201700664] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yuanyuan Wang
- College of Chemistry & Pharmacy; Northwest A&F University; Yangling 712100 P.R. China
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP; Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences; Lanzhou 730000 P.R. China
| | - Liyan Fu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP; Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences; Lanzhou 730000 P.R. China
| | - Huimin Qi
- College of Chemistry & Pharmacy; Northwest A&F University; Yangling 712100 P.R. China
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP; Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences; Lanzhou 730000 P.R. China
| | - Shu-Wei Chen
- College of Chemistry & Pharmacy; Northwest A&F University; Yangling 712100 P.R. China
| | - Yuehui Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP; Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences; Lanzhou 730000 P.R. China
| |
Collapse
|
8
|
Masson SWC, Hedges CP, Devaux JBL, James CS, Hickey AJR. Mitochondrial glycerol 3-phosphate facilitates bumblebee pre-flight thermogenesis. Sci Rep 2017; 7:13107. [PMID: 29026172 PMCID: PMC5638826 DOI: 10.1038/s41598-017-13454-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/22/2017] [Indexed: 11/27/2022] Open
Abstract
Bumblebees (Bombus terrestris) fly at low ambient temperatures where other insects cannot, and to do so they must pre-warm their flight muscles. While some have proposed mechanisms, none fully explain how pre-flight thermogenesis occurs. Here, we present a novel hypothesis based on the less studied mitochondrial glycerol 3-phosphate dehydrogenase pathway (mGPDH). Using calorimetry, and high resolution respirometry coupled with fluorimetry, we report substrate oxidation by mGPDH in permeabilised flight muscles operates, in vitro, at a high flux, even in the absence of ADP. This may be facilitated by an endogenous, mGPDH-mediated uncoupling of mitochondria. This uncoupling increases ETS activity, which results in increased heat release. Furthermore, passive regulation of this mechanism is achieved via dampened temperature sensitivity of mGPDH relative to other respiratory pathways, and subsequent consumption of its substrate, glycerol 3-phosphate (G3P), at low temperatures. Mitochondrial GPDH may therefore facilitate pre-flight thermogenesis through poor mitochondrial coupling. We calculate this can occur at a sufficient rate to warm flight muscles until shivering commences, and until flight muscle function is adequate for bumblebees to fly in the cold.
Collapse
Affiliation(s)
- Stewart W C Masson
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland, 1010, New Zealand
| | - Christopher P Hedges
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland, 1010, New Zealand
- Institute of Sport, Exercise and Active Living, Victoria University, Melbourne, VIC, Australia
| | - Jules B L Devaux
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland, 1010, New Zealand
| | - Crystal S James
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland, 1010, New Zealand
| | - Anthony J R Hickey
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland, 1010, New Zealand.
| |
Collapse
|
9
|
Hassan HA, Rani S, Fatima T, Kiani FA, Fischer S. Effect of protonation on the mechanism of phosphate monoester hydrolysis and comparison with the hydrolysis of nucleoside triphosphate in biomolecular motors. Biophys Chem 2017; 230:27-35. [PMID: 28941815 DOI: 10.1016/j.bpc.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/31/2017] [Accepted: 08/13/2017] [Indexed: 11/25/2022]
Abstract
Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the OaH bond of the attacking water molecule, and the POl bond of the substrate (Oa and Ol stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of OaH and POl bonds occurs simultaneously, whereas in the sequential mechanism, the OaH and POl bonds break at different stages of the reaction. To understand how protonation affects the mechanism of hydrolysis of phosphate monoester, we have studied the mechanism of hydrolysis of protonated and deprotonated phosphate monoester at M06-2X/6-311+G**//M06-2X/6-31+G*+ZPE level of theory (where ZPE stands for zero point energy). Our calculations show that in both protonated and deprotonated cases, the breaking of the water OaH bond occurs before the breaking of the POl bond. Because the two events are not separated by a stable intermediate, the mechanism can be categorized as semi-concurrent. The overall energy barrier is 41kcalmol-1 in the unprotonated case. Most (5/6th) of this is due to the initial breaking of the water OaH bond. This component is lowered from 34 to 25kcalmol-1 by adding one proton to the phosphate. The rest of the overall energy barrier comes from the subsequent breaking of the POl bond and is not sensitive to protonation. This is consistent with previous findings about the effect of triphosphate protonation on the hydrolysis, where the equivalent protonation (on the γ-phosphate) was seen to lower the barrier of breaking the water OaH bond and to have little effect on the POl bond breaking. Hydrolysis pathways of phosphate monoester with initial breaking of the POl bond could not be found here. This is because the leaving group in phosphate monoester cannot be protonated, unlike in triphosphate hydrolysis, where protonation of the β- and γ-phosphates had been shown to promote a mechanism where the POl bond breaks before the OaH bond does. We also point out that the charge shift due to POl bond breaking during sequential ATP hydrolysis in bio-molecular motors onsets the week unbinding of hydrolysis product that finally leads to the product release during power stroke.
Collapse
Affiliation(s)
- Hammad Ali Hassan
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Sadaf Rani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Tabeer Fatima
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan; Department of Biotechnology, University of Gujrat Sialkot Sub Campus, 51310 Sialkot, Pakistan
| | - Farooq Ahmad Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan; Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany street, 02118 Boston, MA, United States.
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany
| |
Collapse
|
10
|
Takahashi H, Umino S, Miki Y, Ishizuka R, Maeda S, Morita A, Suzuki M, Matubayasi N. Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions. J Phys Chem B 2017; 121:2279-2287. [PMID: 28222598 DOI: 10.1021/acs.jpcb.7b00637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy, ΔGhyd, of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd. It was revealed that the electronic-state contribution in ΔGhyd is largely negative (favorable) upon hydrolysis, due to the reduction of electrostatic repulsion accompanying the breakage of the P-O bond. In contrast, the solvation effect was found to be strongly more favorable on the reactant side. Thus, we showed that a drastic compensation of the two opposite effects takes place, leading to the modest value of ΔGhyd at each number of excess electrons examined. The computational analyses were also conducted for pyrophosphate ions (PPi), and the parallelism between the ATP and PPi hydrolyses was confirmed. Classical molecular dynamics simulation was further carried out to discuss the effect of the solvent environment; the insensitivity of ΔGhyd to the number of excess electrons was seen to hold in solvent water and ethanol.
Collapse
Affiliation(s)
- Hideaki Takahashi
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Satoru Umino
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Yuji Miki
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Ryosuke Ishizuka
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Shu Maeda
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Makoto Suzuki
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , Sendai, Miyagi 980-8579, Japan
| | - Nobuyuki Matubayasi
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
11
|
Xu L, Xu Q, Guo X, Ying Y, Wu Y, Wen Y, Yang H. Facile synthesis of Au/Al 2O 3nanocomposites for improving the detection sensitivity of adenosine triphosphate. RSC Adv 2017. [DOI: 10.1039/c7ra03683c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alumina is widely recognized as chemically inert, and resistant to oxidation and high temperature.
Collapse
Affiliation(s)
- Li Xu
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Qin Xu
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Xiaoyu Guo
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Ye Ying
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Yiping Wu
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Ying Wen
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| | - Haifeng Yang
- The Education Ministry Key Lab of Resource Chemistry
- Shanghai Key Laboratory of Rare Earth Functional Materials
- Shanghai Municipal Education Committee
- Key Laboratory of Molecular Imaging Probes and Sensors
- Department of Chemistry
| |
Collapse
|
12
|
Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism. Proc Natl Acad Sci U S A 2014; 111:17851-6. [PMID: 25453082 DOI: 10.1073/pnas.1419486111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The rotary motor enzyme FoF1-ATP synthase uses the proton-motive force across a membrane to synthesize ATP from ADP and Pi (H2PO4(-)) under cellular conditions that favor the hydrolysis reaction by a factor of 2 × 10(5). This remarkable ability to drive a reaction away from equilibrium by harnessing an external force differentiates it from an ordinary enzyme, which increases the rate of reaction without shifting the equilibrium. Hydrolysis takes place in the neighborhood of one conformation of the catalytic moiety F1-ATPase, whose structure is known from crystallography. By use of molecular dynamics simulations we trap a second structure, which is rotated by 40° from the catalytic dwell conformation and represents the state associated with ATP binding, in accord with single-molecule experiments. Using the two structures, we show why Pi is not released immediately after ATP hydrolysis, but only after a subsequent 120° rotation, in agreement with experiment. A concerted conformational change of the α3β3 crown is shown to induce the 40° rotation of the γ-subunit only when the βE subunit is empty, whereas with Pi bound, βE serves as a latch to prevent the rotation of γ. The present results provide a rationalization of how F1-ATPase achieves the coupling between the small changes in the active site of βDP and the 40° rotation of γ.
Collapse
|
13
|
Zhou JY, Lu GX. L-Arginine and zinc ion effect on recognition and hydrolysis rate of adenosine 5′-triphosphate. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.713943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jin-Ying Zhou
- a State Key Laboratory for Oxo Synthesis and Selective Oxidation , Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences , Lanzhou , Gansu 730000 , China
- b Graduate University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Gong-Xuan Lu
- a State Key Laboratory for Oxo Synthesis and Selective Oxidation , Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences , Lanzhou , Gansu 730000 , China
| |
Collapse
|
14
|
Rosenfeld EV. The interrelation between mechanical characteristics of contracting muscle, cross-bridge internal structure, and the mechanism of chemomechanical energy transduction. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:733-53. [PMID: 22930317 DOI: 10.1007/s00249-012-0849-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 06/01/2012] [Accepted: 08/03/2012] [Indexed: 11/28/2022]
Abstract
The cross-bridge working stroke is regarded as a continuous (without jumps) change of myosin head internal state under the action of a force exerted within the nucleotide-binding site. Involvement of a concept of continuous cross-bridge conformation enables discussion of the nature of the force propelling muscle, and the Coulomb repulsion of like-charged adenosine triphosphate (ATP) fragments ADP(2-) and P (i) (2-) can quite naturally be considered as the source of this force. Two entirely different types of working stroke termination are considered. Along with the fluctuation mechanism, which controls the working stroke duration t (w) at isometric contraction, another interrupt mechanism is initially taken into account. It is triggered when the lever arm shift amounts to the maximal value S ≈ 11 nm, the back door opens, and P(i) crashes out. As a result, t (w) becomes inversely proportional to the velocity v of sliding filaments t (w) ≈ S/v for a wide range of values of v. Principal features of the experimentally observed dependences of force, efficiency, and rate of heat production on velocity and ATP concentration can then be reproduced by fitting a single parameter: the velocity-independent time span t (r) between the termination of the last and beginning of the next working stroke. v becomes the principal variable of the model, and the muscle force changes under external load are determined by variations in v rather than in the tension of filaments. The Boltzmann equation for an ensemble of cross-bridges is obtained, and some collective effects are discussed.
Collapse
Affiliation(s)
- E V Rosenfeld
- Institute of Metal Physics, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia.
| |
Collapse
|
15
|
Takahashi H, Omi A, Morita A, Matubayasi N. Simple and exact approach to the electronic polarization effect on the solvation free energy: Formulation for quantum-mechanical/ molecular-mechanical system and its applications to aqueous solutions. J Chem Phys 2012; 136:214503. [DOI: 10.1063/1.4722347] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
16
|
Li M, Zhang J, Suri S, Sooter LJ, Ma D, Wu N. Detection of adenosine triphosphate with an aptamer biosensor based on surface-enhanced Raman scattering. Anal Chem 2012; 84:2837-42. [PMID: 22380526 DOI: 10.1021/ac203325z] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A simple, ultrasensitive, highly selective, and reagent-free aptamer-based biosensor has been developed for quantitative detection of adenosine triphosphate (ATP) using surface-enhanced Raman scattering (SERS). The sensor contains a SERS probe made of gold nanostar@Raman label@SiO(2) core-shell nanoparticles in which the Raman label (malachite green isothiocyanate, MGITC) molecules are sandwiched between a gold nanostar core and a thin silica shell. Such a SERS probe brings enhanced signal and low background fluorescence, shows good water-solubility and stability, and exhibits no sign of photobleaching. The aptamer labeled with the SERS probe is designed to hybridize with the cDNA on a gold film to form a rigid duplex DNA. In the presence of ATP, the interaction between ATP and the aptamer results in the dissociation of the duplex DNA structure and thereby removal of the SERS probe from the gold film, reducing the Raman signal. The response of the SERS biosensor varies linearly with the logarithmic ATP concentration up to 2.0 nM with a limit of detection of 12.4 pM. Our work has provided an effective method for detection of small molecules with SERS.
Collapse
Affiliation(s)
- Ming Li
- Department of Mechanical and Aerospace Engineering, WVNano Initiative, West Virginia University, Morgantown, West Virginia 26506-6106, United States
| | | | | | | | | | | |
Collapse
|
17
|
Sankaranarayanan K, Dhathathreyan A, Krägel J, Miller R. Interfacial viscoelasticity of myoglobin at air/water and air/solution interfaces: role of folding and clustering. J Phys Chem B 2012; 116:895-902. [PMID: 22176527 DOI: 10.1021/jp2100733] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This study describes the folding and organization of myoglobin (Mb) at the solution/air interface at different pH values of 2.5, 3.5, 5.5, 7.5, and 8.5. Dynamic surface tension and the associated dilational and shear viscoelasticity for Mb at these pH's have been studied using a sinusoidal surface compression and expansion for frequencies ranging from 0.01 to 0.4 Hz. The changes in dilational viscosity, elasticity, and fluorescence lifetime measurements have been related to the conformational changes of the protein films at the interface. It is observed that while acid-induced denaturation of the protein does not lead to large changes in dilational properties, the shear properties on the other hand are strongly influenced by it, and the protein behaves like a shear-thickening fluid. At higher pH, particularly at the isoelectric point, Mb is pseudoplastic indicating an increase in the shear viscosity. These results are strongly suggestive of formation of hydrophobic clusters at the protein-buffer interface because of the change in the overall charge distributions.
Collapse
|
18
|
Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase. Proc Natl Acad Sci U S A 2011; 108:20550-5. [PMID: 22143769 DOI: 10.1073/pnas.1117024108] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Understanding the nature of energy transduction in life processes requires a quantitative description of the energetics of the conversion of ATP to ADP by ATPases. Previous attempts to do so have provided an interesting insight but could not account for the rotary mechanism by a nonphenomenological structure/energy description. In particular it has been very challenging to account for the observations of the 80° and 40° rotational substates, without any prior information about such states in the simulation procedure. Here we use a coarse-grained model of F1-ATPase and generate, without the adjustment of phenomenological parameters, a structure-based free energy landscape that reproduces the energetics of the mechanochemical process. It is found that the landscape along the relevant rotary path is determined by the electrostatic free energy and not by steric effects. Furthermore, the generated surface and the corresponding Langevin dynamics simulations identify a hidden conformational barrier that provides a new fundamental interpretation of the catalytic dwell and illuminate the nature of the energy conversion process.
Collapse
|
19
|
|
20
|
Giusti LA, Machado VG. A non-enzymatic model based on an acyl transfer reaction for the formation of energy-rich acetyl phosphate in organic solvents and in a biphasic system. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
21
|
Abstract
ATP hydrolysis is the driving force of many life processes, yet the exact nature of and contributions to the energetics of this reaction are far from being clear. In particular, it is unclear how much of the driving force of this reaction is due to the separation of the already dissociated ADP + P(i) moieties rather than to the chemical event. This fundamental issue is explored here by ab initio calculations that use different solvation models, and it is found that, while the calculations are sensitive to the theoretical approach used, it is quite likely that the dissociation of the charged fragments makes a significant contribution to the energetics of ATP hydrolysis.
Collapse
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry (SGM 418), University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | | |
Collapse
|
22
|
Lervik A, Bresme F, Kjelstrup S, Bedeaux D, Miguel Rubi J. Heat transfer in protein-water interfaces. Phys Chem Chem Phys 2010; 12:1610-7. [PMID: 20126777 DOI: 10.1039/b918607g] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate using transient non-equilibrum molecular dynamics simulation the temperature relaxation process of three structurally different proteins in water, namely; myoglobin, green fluorescence protein (GFP) and two conformations of the Ca(2+)-ATPase protein. By modeling the temperature relaxation process using the solution of the heat diffusion equation we compute the thermal conductivity and thermal diffusivity of the proteins, as well as the thermal conductance of the protein-water interface. Our results indicate that the temperature relaxation of the protein can be described using a macroscopic approach. The protein-water interface has a thermal conductance of the order of 100-270 MW K(-1) m(-2), characteristic of water-hydrophilic interfaces. The thermal conductivity of the proteins is of the order of 0.1-0.2 W K(-1) m(-1) as compared with approximately 0.6 W K(-1) m(-1) for water, suggesting that these proteins can develop temperature gradients within the biomolecular structures that are larger than those of aqueous solutions. We find that the thermal diffusivity of the transmembrane protein, Ca(2+)-ATPase is about three times larger than that of myoglobin or GFP. Our simulation shows that the Kapitza length of these structurally different proteins is of the order of 1 nm, showing that the protein-water interface should play a major role in defining the thermal relaxation of biomolecules.
Collapse
Affiliation(s)
- Anders Lervik
- Department of Chemistry, Imperial College London, London, UKSW7 2AZ
| | | | | | | | | |
Collapse
|
23
|
Nath SS, Nath S. Energy transfer from adenosine triphosphate: quantitative analysis and mechanistic insights. J Phys Chem B 2009; 113:1533-7. [PMID: 19143490 DOI: 10.1021/jp809678n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ATP-ADP thermodynamic cycle is the fundamental mode of energy exchange in oxidative phosphorylation, photophosphorylation, muscle contraction, and intracellular transport by various molecular motors and is therefore of vital importance in biological energy transduction and storage. Following a recent suggestion in the pages of this journal (Ross, J. J. Phys. Chem. B 2006, 110, 6987-6990), we have carried out a simple quantitative analysis of a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP). The simulation provides new insights into the mechanistic events following terminal phosphorus-oxygen bond cleavage during ATP hydrolysis. This approach also allows for the division of the energy-transfer process into elementary steps and for the prediction of the distribution of the standard-state Gibbs free energy of the overall ATP hydrolysis process among the various steps of substrate binding, bond cleavage, and product release in the enzymatic cycle, which had proved very difficult to specify previously. These predictions are consistent with available experimental data on ATP hydrolysis by protein biomolecular machines. The fundamental biological implications arising from our results are also discussed in detail. The aspects considered in this work enable us to look at the entire process of ATP synthesis/hydrolysis and energy transduction and storage in various biological molecular machines in a logically consistent and unified way.
Collapse
Affiliation(s)
- Sarang S Nath
- Science Group, The Mother's International School, Sri Aurobindo Marg, Hauz Khas, New Delhi 110016, India
| | | |
Collapse
|
24
|
The new unified theory of ATP synthesis/hydrolysis and muscle contraction, its manifold fundamental consequences and mechanistic implications and its applications in health and disease. Int J Mol Sci 2008; 9:1784-1840. [PMID: 19325832 PMCID: PMC2635747 DOI: 10.3390/ijms9091784] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 08/18/2008] [Accepted: 09/02/2008] [Indexed: 11/17/2022] Open
Abstract
Complete details of the thermodynamics and molecular mechanisms of ATP synthesis/hydrolysis and muscle contraction are offered from the standpoint of the torsional mechanism of energy transduction and ATP synthesis and the rotation-uncoiling-tilt (RUT) energy storage mechanism of muscle contraction. The manifold fundamental consequences and mechanistic implications of the unified theory for oxidative phosphorylation and muscle contraction are explained. The consistency of current mechanisms of ATP synthesis and muscle contraction with experiment is assessed, and the novel insights of the unified theory are shown to take us beyond the binding change mechanism, the chemiosmotic theory and the lever arm model. It is shown from first principles how previous theories of ATP synthesis and muscle contraction violate both the first and second laws of thermodynamics, necessitating their revision. It is concluded that the new paradigm, ten years after making its first appearance, is now perfectly poised to replace the older theories. Finally, applications of the unified theory in cell life and cell death are outlined and prospects for future research are explored. While it is impossible to cover each and every specific aspect of the above, an attempt has been made here to address all the pertinent details and what is presented should be sufficient to convince the reader of the novelty, originality, breakthrough nature and power of the unified theory, its manifold fundamental consequences and mechanistic implications, and its applications in health and disease.
Collapse
|
25
|
Starikov EB, Panas I, Nordén B. Chemical-to-Mechanical Energy Conversion in Biomacromolecular Machines: A Plasmon and Optimum Control Theory for Directional Work. 1. General Considerations. J Phys Chem B 2008; 112:8319-29. [DOI: 10.1021/jp801580d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evgeni B. Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Itai Panas
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| |
Collapse
|
26
|
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proc Natl Acad Sci U S A 2008; 105:1192-7. [PMID: 18216260 DOI: 10.1073/pnas.0708746105] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
F(o)F(1)-ATP synthase manufactures the energy "currency," ATP, of living cells. The soluble F(1) portion, called F(1)-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level of detail how the conformational changes of the catalytic beta-subunits act on the gamma-subunit through repulsive van der Waals interactions to generate a torque that drives unidirectional rotation, as observed experimentally. The simulations suggest that the calculated 85 degrees substep rotation is driven primarily by ATP binding and that the subsequent 35 degrees substep rotation is produced by product release from one beta-subunit and a concomitant binding pocket expansion of another beta-subunit. The results of the simulation agree with single-molecule experiments [see, for example, Adachi K, et al. (2007) Cell 130:309-321] and support a tri-site rotary mechanism for F(1)-ATPase under physiological condition.
Collapse
|