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Jana AK, Keskin R, Yaşar F. Molecular Insight into the Effect of HIV-TAT Protein on Amyloid-β Peptides. ACS OMEGA 2024; 9:27480-27491. [PMID: 38947850 PMCID: PMC11209880 DOI: 10.1021/acsomega.4c02643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 07/02/2024]
Abstract
Increased deposition of amyloid-β (Aβ) plaques in the brain is a frequent pathological feature observed in human immunodeficiency virus (HIV)-positive patients. Emerging evidence indicates that HIV regulatory proteins, particularly the transactivator of transcription (TAT) protein, could interact with Aβ peptide, accelerating the formation of Aβ plaques in the brain and potentially contributing to the onset of Alzheimer's disease in individuals with HIV infection. Nevertheless, the molecular mechanisms underlying these processes remain unclear. In the present study, we have used long all-atom molecular dynamics simulations to probe the direct interactions between the TAT protein and Aβ peptide at the molecular level. Sampling over 28.0 μs, our simulations show that TAT protein induces a shift in the Aβ monomer ensemble toward elongated conformations, exposing aggregation-prone regions on the surface and thereby inducing subsequent aggregation. TAT protein also appears to enhance the stability of preformed Aβ fibrils, while increasing the β-sheet content within these fibrils. Our atomistically detailed simulations qualitatively agree with previous in vitro and in vivo studies. Importantly, our simulations identify key interactions between Aβ and the TAT protein that drive the Aβ aggregation process and stabilize the preformed Aβ aggregates, which are particularly challenging to obtain through current experimental techniques.
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Affiliation(s)
- Asis K. Jana
- Department
of Microbiology and Biotechnology, Sister
Nivedita University, Kolkata 700156, India
| | - Recep Keskin
- Department
of Physics Engineering, Hacettepe University, Ankara 06800, Türkiye
| | - Fatih Yaşar
- Department
of Physics Engineering, Hacettepe University, Ankara 06800, Türkiye
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2
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Jana AK, Güven Ö, Yaşar F. The stability and dynamics of the Aβ40/Aβ42 interlaced mixed fibrils. J Biomol Struct Dyn 2023:1-14. [PMID: 37964619 DOI: 10.1080/07391102.2023.2280765] [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: 06/21/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
The accumulation of fibrillar amyloid-β (Aβ) aggregates in the brain, predominantly comprising 40- and 42-residue amyloid-β (Aβ40 and Aβ42), is a major pathological hallmark of Alzheimer's disease (AD). Aβ40 and Aβ42 naturally coexist in the brain under normal physiological conditions, and their interplay is generally considered to be a critical factor in the progression of AD. In addition to forming homogeneous oligomers and fibrils, Aβ40 and Aβ42 are also reported to co-assemble into hetero-oligomers and interlaced mixed fibrils, as evidenced by solid-state nuclear magnetic resonance spectroscopy (NMR), high molecular weight mass spectrometry and cross-seeding experiments. However, the exact molecular mechanisms underlying these processes remain unclear. In this study, we have used a recently resolved structurally uniform 1:1 mixture of Aβ40/Aβ42 interlaced mixed fibril as a prototype to gain insights into the molecular-level interactions between Aβ40 and Aβ42. We employed fully atomistic molecular dynamics simulation and compared the results with a homogeneous U-shaped Aβ40 fibrillar model. Our simulations using two different force fields provide conclusive evidence that the Aβ40/Aβ42 interlaced mixed fibril is energetically more favorable than the homogeneous Aβ40 fibrillar model. Furthermore, we also show that the increase in stability observed in the mixed model stems primarily from the packing interfaces and the stacking interfaces between C-termini. Our simulation results provide valuable mechanistic insights that are not readily accessible in experiment and could have significant implications for both the pathogenesis of AD and the development of current therapeutic strategies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asis K Jana
- Department of Microbiology and Biotechnology, Sister Nivedita University, Kolkata, West Bengal, India
| | - Özgür Güven
- Department of Physics Engineering, Hacettepe University, Ankara, Türkiye
| | - Fatih Yaşar
- Department of Physics Engineering, Hacettepe University, Ankara, Türkiye
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3
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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4
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Chapman J, Zoica Dinu C. Assessment of Enzyme Functionality at Metal-Organic Framework Interfaces Developed through Molecular Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1750-1763. [PMID: 36692448 DOI: 10.1021/acs.langmuir.2c02347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The catalytic efficiency and unrivaled selectivity with which enzymes convert substrates to products have been tapped for widespread chemical transformations within biomedical technology, biofuel production, gas sensing, and the upgrading of commodity chemicals, just to name a few. However, the feasibility of enzymes implementation is challenged by the lack of reusability and loss of native catalytic activity due to the irreversible biocatalyst denaturation at high temperatures and in the presence of industrial solvents. Enzyme immobilization, a prerequisite for enzyme reusability, offers controllable strategies for increased functional viability of the biocatalyst in a synthetic environment. Herein we used molecular dynamics (MD) simulations and probed the noncovalent interactions between model enzymes of technological interest, i.e., carbonic anhydrase (CA) and myeloperoxidase (MPO), with selected metal-organic frameworks (MOFs; MIL-160 and ZIF-8) of proven industrial implementation. We found that the CA and MPO can bind to MIL-160 at optimal binding energies of 201 and 501 kJ mol-1, respectively, that are strongly influenced by the increased incidence of hydrogen bonding between enzymes and the frameworks. The free energy of binding of enzymes to ZIF-8, on the other hand, was found to be less strongly influenced by hydrogen bonding networks relative to the occurrence of hydrophobic-hydrophobic interactions that yielded 106 kJ mol-1 for CA and 201 kJ mol-1 for MPO.
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Affiliation(s)
- Jordan Chapman
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, United States
| | - Cerasela Zoica Dinu
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, West Virginia 26506-6070, United States
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5
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Bilal M, Ashraf SS, Ferreira LFR, Cui J, Lou WY, Franco M, Iqbal HMN. Nanostructured materials as a host matrix to develop robust peroxidases-based nanobiocatalytic systems. Int J Biol Macromol 2020; 162:1906-1923. [PMID: 32818568 DOI: 10.1016/j.ijbiomac.2020.08.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/05/2023]
Abstract
Nanostructured materials constitute an interesting and novel class of support matrices for the immobilization of peroxidase enzymes. Owing to the high surface area, robust mechanical stability, outstanding optical, thermal, and electrical properties, nanomaterials have been rightly perceived as immobilization matrices for enzyme immobilization with applications in diverse areas such as nano-biocatalysis, biosensing, drug delivery, antimicrobial activities, solar cells, and environmental protection. Many nano-scale materials have been employed as support matrices for the immobilization of different classes of enzymes. Nanobiocatalysts, enzymes immobilized on nano-size materials, are more stable, catalytically robust, and could be reused and recycled in multiple reaction cycles. In this review, we illustrate the unique structural/functional features and potentialities of nanomaterials-immobilized peroxidase enzymes in different biotechnological applications. After a comprehensive introduction to the immobilized enzymes and nanocarriers, the first section reviewed carbonaceous nanomaterials (carbon nanotube, graphene, and its derivatives) as a host matrix to constitute robust peroxidases-based nanobiocatalytic systems. The second half covers metallic nanomaterials (metals, and metal oxides) and some other novel materials as host carriers for peroxidases immobilization. The next section vetted the potential biotechnological applications of the resulted nanomaterials-immobilized robust peroxidases-based nanobiocatalytic systems. Concluding remarks, trends, and future recommendations for nanomaterial immobilized enzymes are also given.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - S Salman Ashraf
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Luiz Fernando Romanholo Ferreira
- Graduate Program in Process Engineering, Tiradentes University, Av. Murilo Dantas 300, Farolândia, 49032-490 Aracaju, SE, Brazil; Institute of Technology and Research, Av. Murilo Dantas 300 - Prédio do ITP, Farolândia, 49032-490 Aracaju, SE, Brazil
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No 29, 13th, Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, China
| | - Wen-Yong Lou
- Lab of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China
| | - Marcelo Franco
- Department of Exact and Technological Sciences, State University of Santa Cruz, 45654-370 Ilhéus, Brazil
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
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Ariaeenejad S, Lanjanian H, Motamedi E, Kavousi K, Moosavi-Movahedi AA, Hosseini Salekdeh G. The Stabilizing Mechanism of Immobilized Metagenomic Xylanases on Bio-Based Hydrogels to Improve Utilization Performance: Computational and Functional Perspectives. Bioconjug Chem 2020; 31:2158-2171. [DOI: 10.1021/acs.bioconjchem.0c00361] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
| | - Hossein Lanjanian
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, 13145, Iran
| | - Elaheh Motamedi
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
| | - Kaveh Kavousi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, 13145, Iran
| | | | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, New South Wales, Australia
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7
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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8
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Munasinghe A, Baker SL, Lin P, Russell AJ, Colina CM. Structure-function-dynamics of α-chymotrypsin based conjugates as a function of polymer charge. SOFT MATTER 2020; 16:456-465. [PMID: 31803897 DOI: 10.1039/c9sm01842e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The field of protein-polymer conjugates has suffered from a lack of predictive tools and design guidelines to synthesize highly active and stable conjugates. In order to develop this type of information, structure-function-dynamics relationships must be understood. These relationships depend strongly on protein-polymer interactions and how these influence protein dynamics and conformations. Probing nanoscale interactions is experimentally difficult, but computational tools, such as molecular dynamics simulations, can easily obtain atomic resolution. Atomistic molecular dynamics simulations were used to study α-chymotrypsin (CT) densely conjugated with either zwitterionic, positively charged, or negatively charged polymers. Charged polymers interacted with the protein surface to varying degrees and in different regions of the polymer, depending on their flexibilities. Specific interactions of the negatively charged polymer with CT caused structural deformations in CT's substrate binding pocket and active site while no deformations were observed for zwitterionic and positively charged polymers. Attachment of polymers displaced water molecules from CT's surface into the polymer phase and polymer hydration correlated with the Hofmeister series.
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Affiliation(s)
- Aravinda Munasinghe
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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10
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Thamwattana N, Sarapat P, Chan Y. Mechanics and dynamics of lysozyme immobilisation inside nanotubes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:265901. [PMID: 30917355 DOI: 10.1088/1361-648x/ab13c9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lysozyme is an enzyme often used as an antibacterial agent in food industries and biochemical and pharmaceutical laboratories. Immobilisation of lysozyme by encapsulating in a nanotube has received much interest as it can enhance stability of the enzyme in ambient condition. Experimentally, various types of nanotubes have been proposed as a host for lysozyme. Here, we mathematically model the immobilisation process and the interaction between lysozyme and various types of nanotubes in order to compare the effectiveness of different nanotube materials. In this paper, we consider boron nitride, carbon, silicon, silicon carbide and titania nanotubes. For each type of nanotubes, we determine the critical radius that will maximise the interaction between the lysozyme molecule and the nanotube. Our results suggest that titania nanotube stands out as the most promising candidate for lysozyme storage and delivery. The model presented here can be extended to further investigate the interaction between different types of nanotube materials and protein structures for the development of effective molecular storage.
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Affiliation(s)
- Ngamta Thamwattana
- School of Mathematical and Physical Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
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11
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T7 RNA Polymerase Discriminates Correct and Incorrect Nucleoside Triphosphates by Free Energy. Biophys J 2019; 114:1755-1761. [PMID: 29694856 DOI: 10.1016/j.bpj.2018.02.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/17/2018] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
RNA polymerase (RNAP) is the primary machine responsible for transcription. Its ability to distinguish between correct (cognate) and incorrect (noncognate) nucleoside triphosphates (NTPs) is important for fidelity control in transcription. In this work, we investigated the substrate selection mechanism of T7 RNAP from the perspective of energetics. The dissociation free energies were determined for matched and unmatched base pairs in the preinsertion complex using the umbrella sampling method. A clear hydrogen-bond-rupture peak is observed in the potential of mean force curve for a matched base pair, whereas no such peaks are present in the position of mean force profiles for unmatched ones. The free-energy barrier could prevent correct substrates from being separated from the active site. Therefore, when NTPs diffuse into the active site, correct ones will stay for chemistry once they establish effective base pairing contacts with the template nucleotide, whereas incorrect ones will be withdrawn from the active site and rejected back to solution. This result provides an important energy evidence for the substrate selection mechanism of RNAP. Then we elucidated energetics and molecular details for correct NTP binding to the active site of the insertion complex. Our observations reveal that strong interactions act on the triphosphate of NTP to constrain its movement, whereas relatively weak interactions serve to position the base in the correct conformation. Triple interactions, hydrophobic contacts from residues M635 and Y639, base stacking from the 3' RNA terminal nucleotide, and base pairing from the template nucleotide act together to position the NTP base in a catalytically competent conformation. At last, we observed that incorrect NTPs cannot be as well-stabilized as the correct one in the active site when they are misincorporated in the insertion site. It is expected that our work can be helpful for comprehensively understanding details of this basic step in genetic transcription.
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12
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Zaboli M, Raissi H, Zaboli M, Farzad F, Torkzadeh-Mahani M. Stabilization of d-lactate dehydrogenase diagnostic enzyme via immobilization on pristine and carboxyl-functionalized carbon nanotubes, a combined experimental and molecular dynamics simulation study. Arch Biochem Biophys 2019; 661:178-186. [DOI: 10.1016/j.abb.2018.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 12/29/2022]
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13
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Rasoolzadeh R, Mehrnejad F, Taghdir M, Yaghmaei P. Effects of single-walled carbon nanotube on the conformation of human hepcidin: molecular dynamics simulation and binding free energy calculations. J Biomol Struct Dyn 2018; 37:2125-2132. [DOI: 10.1080/07391102.2018.1477624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Reza Rasoolzadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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14
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Bologna F, Mattioli EJ, Bottoni A, Zerbetto F, Calvaresi M. Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C 60-Lysozyme Model. ACS OMEGA 2018; 3:13782-13789. [PMID: 31458078 PMCID: PMC6644377 DOI: 10.1021/acsomega.8b01888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.
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Affiliation(s)
- Fabio Bologna
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics. Sci Rep 2018; 8:12976. [PMID: 30154518 PMCID: PMC6113251 DOI: 10.1038/s41598-018-31234-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
The effects of phosphorylation of a serine residue on the structural and dynamic properties of Ras-like protein, Rap, and its interactions with effector protein Ras binding domain (RBD) of Raf kinase, in the presence of GTP, are investigated via molecular dynamics simulations. The simulations show that phosphorylation significantly effects the dynamics of functional loops of Rap which participate in the stability of the complex with effector proteins. The effects of phosphorylation on Rap are significant and detailed conformational analysis suggest that the Rap protein, when phosphorylated and with GTP ligand, samples different conformational space as compared to non-phosphorylated protein. In addition, phosphorylation of SER11 opens up a new cavity in the Rap protein which can be further explored for possible drug interactions. Residue network analysis shows that the phosphorylation of Rap results in a community spanning both Rap and RBD and strongly suggests transmission of allosteric effects of local alterations in Rap to distal regions of RBD, potentially affecting the downstream signalling. Binding free energy calculations suggest that phosphorylation of SER11 residue increases the binding between Rap and Raf corroborating the network analysis results. The increased binding of the Rap-Raf complex can have cascading effects along the signalling pathways where availability of Raf can influence the oncogenic effects of Ras proteins. These simulations underscore the importance of post translational modifications like phosphorylation on the functional dynamics in proteins and can be an alternative to drug-targeting, especially in notoriously undruggable oncoproteins belonging to Ras-like GTPase family.
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16
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Zhang L, Yuan Y, Ren T, Guo Y, Li C, Pu X. Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor. Sci Rep 2018; 8:7824. [PMID: 29777138 PMCID: PMC5959861 DOI: 10.1038/s41598-018-26105-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Olfactory receptor (OR)-based bioelectronic nose is a new type of bio-affinity sensor applied for detecting numerous odorant molecules. In order to elucidate the effect of the adsorption of nanomaterial carriers on the receptor structure and its selectivity to odors, we used a systematic computation-scheme to study two OR models immobilized onto carbon nanotube. Our result indicates that there is a multistep OR-adsorption process driven by hydrophobic interaction. Many allosteric communication pathways exist between the absorbed residues and the pocket ones, leading to a significant shrinkage of the pocket. Consequently, the size-selectivity of the receptor to the odors is changed to some extent. But, the odor size and its hydrophobicity, rather than specific functional groups of the odor, still play a determinant role in binding OR, at least for the 132 odors under study. Regardless of the limitation for the odor size in initial recognition, the different-size odors could induce significant changes in the pocket conformation so that it could better match the pocket space, indicating the importance of the ligand-fit binding. Due to the CNT-induced shrinkage of the pocket, the CNT immobilization could increase the binding affinity through enhancing van der Waals interaction, in particular for the large odors.
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Affiliation(s)
- Liyun Zhang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu, 610041, P.R. China
| | - Tian Ren
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, 610064, P.R. China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China.
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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18
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Wu S, Li L, Li Q. Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation. Biophys J 2017; 112:2253-2260. [PMID: 28591598 PMCID: PMC5474740 DOI: 10.1016/j.bpj.2017.04.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 04/11/2017] [Accepted: 04/24/2017] [Indexed: 11/26/2022] Open
Abstract
In genetic transcription, molecular dynamic details and energetics of NTP binding to the active site of RNA polymerase (RNAP) are poorly understood. In this article, we investigated the NTP binding process in T7 RNAP using all-atom MD simulation combined with the umbrella sampling technique. Based on our simulations, a two-step mechanism was proposed to explain NTP binding: first, substrate NTP in aqueous solution, which carries a magnesium ion, diffuses through a secondary channel of RNAP to attain a pore region, where it undergoes conformational changes to give a correct orientation; next, the NTP establishes initial basepairing contacts with the template nucleoside (TN). Our free-energy calculations suggest that both steps are spontaneous. This mechanism can easily explain the problem of NTP binding with different orientations. Moreover, it is found that the nascent NTP:TN basepair is fragile and easily broken by thermal disturbance. Therefore, we speculate that the fingers domain will be triggered to close, so as to create a steady environment for the next chemical step. The observations from the work provide valuable information for comprehensively understanding the mechanism of the basic step in genetic transcription.
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Affiliation(s)
- Shaogui Wu
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China; State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
| | - Laicai Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China
| | - Quan Li
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, China
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19
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Menon S, Sengupta N. Influence of Hyperglycemic Conditions on Self-Association of the Alzheimer's Amyloid β (Aβ 1-42) Peptide. ACS OMEGA 2017; 2:2134-2147. [PMID: 30023655 PMCID: PMC6044820 DOI: 10.1021/acsomega.7b00018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/08/2017] [Indexed: 06/08/2023]
Abstract
Clinical studies have identified a correlation between type-2 diabetes mellitus and cognitive decrements en route to the onset of Alzheimer's disease (AD). Recent studies have established that post-translational modifications of the amyloid β (Aβ) peptide occur under hyperglycemic conditions; particularly, the process of glycation exacerbates its neurotoxicity and accelerates AD progression. In view of the assertion that macromolecular crowding has an altering effect on protein self-assembly, it is crucial to characterize the effects of hyperglycemic conditions via crowding on Aβ self-assembly. Toward this purpose, fully atomistic molecular dynamics simulations were performed to study the effects of glucose crowding on Aβ dimerization, which is the smallest known neurotoxic species. The dimers formed in the glucose-crowded environment were found to have weaker associations as compared to that of those formed in water. Binding free energy calculations show that the reduced binding strength of the dimers can be mainly attributed to the overall weakening of the dispersion interactions correlated with substantial loss of interpeptide contacts in the hydrophobic patches of the Aβ units. Analysis to discern the differential solvation pattern in the glucose-crowded and pure water systems revealed that glucose molecules cluster around the protein, at a distance of 5-7 Å, which traps the water molecules in close association with the protein surface. This preferential exclusion of glucose molecules and resulting hydration of the Aβ peptides has a screening effect on the hydrophobic interactions, which in turn diminishes the binding strength of the resulting dimers. Our results imply that physical effects attributed to crowded hyperglycemic environments are incapable of solely promoting Aβ self-assembly, indicating that further mechanistic studies are required to provide insights into the self-assembly of post-translationally modified Aβ peptides, known to possess aggravated toxicity, under these conditions.
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Affiliation(s)
- Sneha Menon
- Physical
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Training and Development Complex, CSIR Campus,
CSIR Road, Chennai 600113, India
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
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20
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Atabay M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. Adsorption and immobilisation of human insulin on graphene monoxide, silicon carbide and boron nitride nanosheets investigated by molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1270452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Azarbaijan Shahid Madani University, Tabriz, Iran
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21
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Zhao D, Zhou J. Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes. Phys Chem Chem Phys 2017; 19:986-995. [DOI: 10.1039/c6cp04962a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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22
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Zhang L, Li Y, Yuan Y, Jiang Y, Guo Y, Li M, Pu X. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media. Sci Rep 2016; 6:36838. [PMID: 27874101 PMCID: PMC5118797 DOI: 10.1038/srep36838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/17/2016] [Indexed: 02/04/2023] Open
Abstract
In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.
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Affiliation(s)
- Liyun Zhang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuzhi Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, People's Republic of China
| | - Yuanyuan Jiang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
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23
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De Matteis L, Di Renzo F, Germani R, Goracci L, Spreti N, Tiecco M. α-Chymotrypsin superactivity in quaternary ammonium salt solution: kinetic and computational studies. RSC Adv 2016. [DOI: 10.1039/c6ra07425a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ammonium salts determine an increase of the hydrophobicity of the α-chymotrypsin catalytic site and therefore an improvement of its activity.
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Affiliation(s)
- Laura De Matteis
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67100 Coppito
- Italy
| | - Francesca Di Renzo
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67100 Coppito
- Italy
| | - Raimondo Germani
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- I-06123 Perugia
| | - Laura Goracci
- Laboratory for Chemoinformatics and Molecular Modelling
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- I-06123 Perugia
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67100 Coppito
- Italy
| | - Matteo Tiecco
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- I-06123 Perugia
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24
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Jana AK, Tiwari MK, Vanka K, Sengupta N. Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures. Phys Chem Chem Phys 2016; 18:5910-24. [DOI: 10.1039/c5cp04675k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Underlying causes of the differential polypeptide interactions on carbon nanosurfaces of varying curvatures emerge from a synchronized computational study.
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Affiliation(s)
- Asis K. Jana
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | | | - Kumar Vanka
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Neelanjana Sengupta
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
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25
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Jiang W, Li W, Hong Y, Wang S, Fang B. Cloning, Expression, Mutagenesis Library Construction of Glycerol Dehydratase, and Binding Mode Simulation of Its Reactivase with Ligands. Appl Biochem Biotechnol 2015; 178:739-52. [PMID: 26547853 DOI: 10.1007/s12010-015-1906-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
Abstract
The production of 1, 3-propanediol (1, 3-PD) and 3-hydroxypropionaldehyde (3-HPA) by enzyme reaction has been a hot field, and glycerol dehydratase (GDHt) is the key and rate-limiting enzyme involved in their biosynthesis. The gldABC gene encoding GDHt was cloned from Klebsiella pneumoniae, and the activity of the corresponding proteins expressed extracellularly and intracellularly was 6.8 and 3.2 U/mg, respectively, about six and three times higher than that of the wild strain. The change of amino acids for the β subunit can adjust the length of the Co-N bond and affect the homolysis rate of the Co-C bond to change GDHt activity. The expression plasmid, pET-32a-gldAC (containing no gldB which encodes the β subunit of GDHt), was constructed to build the mutagenesis library to improve the GDHt activity. The binding models of glycerol dehydratase reactivation factor (GDHtR) with ATP, CTP, or GTP were simulated by semi-flexible docking, respectively, and there was almost no difference between them. This research provided the basis for studying the quantitative structure-activity relationships between GDHtR and its ligands, as well as searching inexpensive ligands to replace ATP. These results and methods are of great use in economical and highly efficient production of 3-HPA and 1, 3-PD by the enzyme method.
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Affiliation(s)
- Wei Jiang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Wenjun Li
- Hangzhou DAC Biotech Co., Ltd, Hangzhou, 310000, China
| | - Yan Hong
- Jingdezhen Ceramic Institute of Materials Science and Engineering, Jingde Zhen, 333000, China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China.
- The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, 361005, China.
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