1
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Nakamura I, Amesaka H, Hara M, Yonezawa K, Okamoto K, Kamikubo H, Tanaka S, Matsuo T. Conformation state-specific monobodies regulate the functions of flexible proteins through conformation trapping. Protein Sci 2023; 32:e4813. [PMID: 37861467 PMCID: PMC10659937 DOI: 10.1002/pro.4813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Synthetic binding proteins have emerged as modulators of protein functions through protein-protein interactions (PPIs). Because PPIs are influenced by the structural dynamics of targeted proteins, investigating whether the synthetic-binders-based strategy is applicable for proteins with large conformational changes is important. This study demonstrates the applicability of monobodies (fibronectin type-III domain-based synthetic binding proteins) in regulating the functions of proteins that undergo tens-of-angstroms-scale conformational changes, using an example of the A55C/C77S/V169C triple mutant (Adktm ; a phosphoryl transfer-catalyzing enzyme with a conformational change between OPEN/CLOSED forms). Phage display successfully developed monobodies that recognize the OPEN form (substrate-unbound form), but not the CLOSED form of Adktm . Two OPEN form-specific clones (OP-2 and OP-4) inhibited Adktm kinase activity. Epitope mapping with a yeast-surface display/flow cytometry indicated that OP-2 binds to the substrate-entry side of Adktm , whereas OP-4 binding occurs at another site. Small angle X-ray scattering coupled with size-exclusion chromatography (SEC-SAXS) indicated that OP-4 binds to the hinge side opposite to the substrate-binding site of Adktm , retaining the whole OPEN-form structure of Adktm . Titration of the OP-4-Adktm complex with Ap5 A, a transition-state analog of Adktm , showed that the conformational shift to the CLOSED form was suppressed although Adktm retained the OPEN-form (i.e., substrate-binding ready form). These results show that OP-4 captures and stabilizes the OPEN-form state, thereby affecting the hinge motion. These experimental results indicate that monobody-based modulators can regulate the functions of proteins that show tens-of-angstroms-scale conformational changes, by trapping specific conformational states generated during large conformational change process that is essential for function exertion.
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Affiliation(s)
- Ibuki Nakamura
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
| | - Hiroshi Amesaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Mizuho Hara
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Kento Yonezawa
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Keisuke Okamoto
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Shun‐ichi Tanaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
- Department of Biotechnology, College of Life SciencesRitsumeikan UniversityKusatsuJapan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
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2
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Biros E, Birosova E, Moran CS. Mechanistic considerations for adenosine-lidocaine-magnesium (ALM) in controlling coagulopathy. Trends Pharmacol Sci 2023; 44:324-334. [PMID: 36805364 DOI: 10.1016/j.tips.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/21/2023]
Abstract
Adenosine-lidocaine-magnesium (ALM) mixture is a cardioplegic agent that improves survivability in rodent, but not swine, models of noncompressible torso hemorrhage (NCTH). However, despite protection from comorbid coagulopathy being the one common effect reported in both NCTH models, the underlying prothrombotic mechanism for ALM has not been elucidated in either. Here, we undertook a component-based approach focusing on individual drugs in the mixture to elaborate on the protective mechanism against coagulopathy within the frames of adenosine signaling and metabolic pathways. Additionally, the translational potential of small and large animal models of NCTH for human survival is critically appraised, owing to substantial quantitative/qualitative differences between humans and rodents, particularly regarding the genetics of G protein-coupled receptors (GPCRs) interacting with ALM's constituents.
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Affiliation(s)
- Erik Biros
- College of Medicine and Dentistry, James Cook University, Townsville, Australia.
| | - Eva Birosova
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
| | - Corey S Moran
- College of Medicine and Dentistry, James Cook University, Townsville, Australia; School of Dentistry, The University of Queensland, Herston, Brisbane, Australia
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3
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Zhang Y, Chen M, Lu J, Li W, Wolynes PG, Wang W. Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. J Phys Chem B 2022; 126:6792-6801. [PMID: 36044985 PMCID: PMC9483917 DOI: 10.1021/acs.jpcb.2c03832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Substrate inhibition, whereby enzymatic activity decreases
with
excess substrate after reaching a maximum turnover rate, is among
the most elusive phenomena in enzymatic catalysis. Here, based on
a dynamic energy landscape model, we investigate the underlying mechanism
by performing molecular simulations and frustration analysis for a
model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl
transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these
reveal a kinetic repartitioning mechanism of substrate inhibition,
whereby excess substrate AMP suppresses the population of an energetically
frustrated, but kinetically activated, catalytic pathway going through
a substrate (ATP)-product (ADP) cobound complex with steric incompatibility.
Such a frustrated pathway plays a crucial role in facilitating the
bottleneck product ADP release, and its suppression by excess substrate
AMP leads to a slow down of product release and overall turnover.
The simulation results directly demonstrate that substrate inhibition
arises from the rate-limiting product-release step, instead of the
steps for populating the catalytically competent complex as often
suggested in previous works. Furthermore, there is a tight interplay
between the enzyme conformational equilibrium and the extent of substrate
inhibition. Mutations biasing to more closed conformations tend to
enhance substrate inhibition. We also characterized the key features
of single-molecule enzyme kinetics with substrate inhibition effect.
We propose that the above molecular mechanism of substrate inhibition
may be relevant to other multisubstrate enzymes in which product release
is the bottleneck step.
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Affiliation(s)
- Yangyang Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Mingchen Chen
- Department of Research and Development, neoX Biotech, Beijing 102206, China.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jiajun Lu
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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4
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Chang WH, Huang SH, Lin HH, Chung SC, Tu IP. Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules. FRONTIERS IN BIOINFORMATICS 2021; 1:788308. [PMID: 36303748 PMCID: PMC9580929 DOI: 10.3389/fbinf.2021.788308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
The functions of biological macromolecules are often associated with conformational malleability of the structures. This phenomenon of chemically identical molecules with different structures is coined structural polymorphism. Conventionally, structural polymorphism is observed directly by structural determination at the density map level from X-ray crystal diffraction. Although crystallography approach can report the conformation of a macromolecule with the position of each atom accurately defined in it, the exploration of structural polymorphism and interpreting biological function in terms of crystal structures is largely constrained by the crystal packing. An alternative approach to studying the macromolecule of interest in solution is thus desirable. With the advancement of instrumentation and computational methods for image analysis and reconstruction, cryo-electron microscope (cryo-EM) has been transformed to be able to produce “in solution” structures of macromolecules routinely with resolutions comparable to crystallography but without the need of crystals. Since the sample preparation of single-particle cryo-EM allows for all forms co-existing in solution to be simultaneously frozen, the image data contain rich information as to structural polymorphism. The ensemble of structure information can be subsequently disentangled through three-dimensional (3D) classification analyses. In this review, we highlight important examples of protein structural polymorphism in relation to allostery, subunit cooperativity and function plasticity recently revealed by cryo-EM analyses, and review recent developments in 3D classification algorithms including neural network/deep learning approaches that would enable cryo-EM analyese in this regard. Finally, we brief the frontier of cryo-EM structure determination of RNA molecules where resolving the structural polymorphism is at dawn.
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Affiliation(s)
- Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- *Correspondence: Wei-Hau Chang,
| | | | - Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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5
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Chang J, Zhang C, Cheng H, Tan YW. Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. Int J Mol Sci 2021; 22:ijms22052768. [PMID: 33803409 PMCID: PMC7967156 DOI: 10.3390/ijms22052768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023] Open
Abstract
Protein engineering is actively pursued in industrial and laboratory settings for high thermostability. Among the many protein engineering methods, rational design by bioinformatics provides theoretical guidance without time-consuming experimental screenings. However, most rational design methods either rely on protein tertiary structure information or have limited accuracies. We proposed a primary-sequence-based algorithm for increasing the heat resistance of a protein while maintaining its functions. Using adenylate kinase (ADK) family as a model system, this method identified a series of amino acid sites closely related to thermostability. Single- and double-point mutants constructed based on this method increase the thermal denaturation temperature of the mesophilic Escherichia coli (E. coli) ADK by 5.5 and 8.3 °C, respectively, while preserving most of the catalytic function at ambient temperatures. Additionally, the constructed mutants have improved enzymatic activity at higher temperature.
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Affiliation(s)
- Jian Chang
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
| | - Chengxin Zhang
- School of Life Science, Fudan University, Shanghai 200433, China;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huaqiang Cheng
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
- Correspondence:
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6
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Morrison ZA, Nitz M. Synthesis of C6-substituted UDP-GlcNAc derivatives. Carbohydr Res 2020; 495:108071. [PMID: 32634644 DOI: 10.1016/j.carres.2020.108071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/05/2023]
Abstract
UDP-sugar analogs are useful for the study of glycosyltransferases and the production of unnatural glycans. The preparation of five UDP-GlcNAc derivatives is reported with 6-deoxy, 6-azido, 6-amino, 6-mercapto, or 6-fluoro substitutions. A concise chemoenzymatic synthesis was developed using the kinase NahK (B. longum JCM1217) and the uridyl transferase GlmU (E. coli K12).
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Affiliation(s)
- Zachary A Morrison
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
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7
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Zhou W, Hankinson CP, Deiters A. Optical Control of Cellular ATP Levels with a Photocaged Adenylate Kinase. Chembiochem 2020; 21:1832-1836. [PMID: 32187807 DOI: 10.1002/cbic.201900757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/20/2020] [Indexed: 02/06/2023]
Abstract
We have developed a new tool for the optical control of cellular ATP concentrations with a photocaged adenylate kinase (Adk). The photocaged Adk is generated by substituting a catalytically essential lysine with a hydroxycoumarin-protected lysine through site-specific unnatural amino acid mutagenesis in both E. coli and mammalian cells. Caging of the critical lysine residue offers complete suppression of Adk's phosphotransferase activity and rapid restoration of its function both in vitro and in vivo upon optical stimulation. Light-activated Adk renders faster rescue of cell growth than chemically inducible expression of wild-type Adk in E. coli as well as rapid ATP depletion in mammalian cells. Thus, caging Adk provides a new tool for direct conditional perturbation of cellular ATP concentrations thereby enabling the investigation of ATP-coupled physiological events in temporally dynamic contexts.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Chasity P Hankinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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8
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Nocek BP, Khusnutdinova AN, Ruszkowski M, Flick R, Burda M, Batyrova K, Brown G, Mucha A, Joachimiak A, Berlicki Ł, Yakunin AF. Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03151] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Boguslaw P. Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, Illinois 60439, United States
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Malgorzata Burda
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Khorcheska Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
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9
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Mazal H, Aviram H, Riven I, Haran G. Effect of ligand binding on a protein with a complex folding landscape. Phys Chem Chem Phys 2018; 20:3054-3062. [PMID: 28721412 DOI: 10.1039/c7cp03327c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Song S, Chang J, Ma C, Tan YW. Single-Molecule Fluorescence Methods to Study Plant Hormone Signal Transduction Pathways. FRONTIERS IN PLANT SCIENCE 2017; 8:1888. [PMID: 29163610 PMCID: PMC5673658 DOI: 10.3389/fpls.2017.01888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 05/15/2023]
Abstract
Plant-hormone-initiated signaling pathways are extremely vital for plant growth, differentiation, development, and adaptation to environmental stresses. Hormonal perception by receptors induces downstream signal transduction mechanisms that lead to plant responses. However, conventional techniques-such as genetics, biochemistry, and physiology methods-that are applied to elucidate these signaling pathways can only provide qualitative or ensemble-averaged quantitative results, and the intrinsic molecular mechanisms remain unclear. The present study developed novel methodologies based on in vitro single-molecule fluorescence assays to elucidate the complete and detailed mechanisms of plant hormone signal transduction pathways. The proposed methods are based on multicolor total internal reflection fluorescence microscopy and a flow cell model for gas environment control. The methods validate the effectiveness of single-molecule approaches for the extraction of abundant information, including oligomerization, specific gas dependence, and the interaction kinetics of different components.
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11
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Ouyang Y, Zhu L, Li Y, Guo M, Liu Y, Cheng J, Zhao J, Wu Y. Architectural plasticity of AMPK revealed by electron microscopy and X-ray crystallography. Sci Rep 2016; 6:24191. [PMID: 27063142 PMCID: PMC4827068 DOI: 10.1038/srep24191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022] Open
Abstract
Mammalian AMP-activated protein kinase (AMPK) acts as an important sensor of cellular energy homeostasis related with AMP/ADP to ATP ratio. The overall architecture of AMPK has been determined in either homotrimer or monomer form by electron microscopy (EM) and X-ray crystallography successively. Accordingly proposed models have consistently revealed a key role of the α subunit linker in sensing adenosine nucleoside binding on the γ subunit and mediating allosteric regulation of kinase domain (KD) activity, whereas there are vital differences in orienting N-terminus of α subunit and locating carbohydrate-binding module (CBM) of β subunit. Given that Mg2+, an indispensable cofactor of AMPK was present in the EM sample preparation buffer however absent when forming crystals, here we carried out further reconstructions without Mg2+ to expectably inspect if this ion may contribute to this difference. However, no essential alteration has been found in this study compared to our early work. Further analyses indicate that the intra-molecular movement of the KD and CBM are most likely due to the flexible linkage of the disordered linkers with the rest portion as well as a contribution from the plasticity in the inter-molecular assembly mode, which might ulteriorly reveal an architectural complication of AMPK.
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Affiliation(s)
- Yan Ouyang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Li Zhu
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yifang Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Miaomiao Guo
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yang Liu
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jin Cheng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jing Zhao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yi Wu
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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12
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Fujii A, Sekiguchi Y, Matsumura H, Inoue T, Chung WS, Hirota S, Matsuo T. Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes. Bioconjug Chem 2015; 26:537-48. [DOI: 10.1021/acs.bioconjchem.5b00026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Akira Fujii
- Graduate
School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yutaka Sekiguchi
- Graduate
School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Hiroyoshi Matsumura
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wen-Sheng Chung
- Department
of Applied Chemistry, National Chiao Tung University, Hsinchu, 30050, Taiwan, Republic of China
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate
School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
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13
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Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D. The energy landscape of adenylate kinase during catalysis. Nat Struct Mol Biol 2015; 22:124-31. [PMID: 25580578 PMCID: PMC4318763 DOI: 10.1038/nsmb.2941] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/26/2014] [Indexed: 12/17/2022]
Abstract
Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.
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Affiliation(s)
- S Jordan Kerns
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Roman V Agafonov
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Young-Jin Cho
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Francesco Pontiggia
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Renee Otten
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Dimitar V Pachov
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Steffen Kutter
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Lien A Phung
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Padraig N Murphy
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Vu Thai
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | | | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts, USA
| | - Dorothee Kern
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
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14
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Purification and characterization of guanylate kinase, a nucleoside monophosphate kinase of Brugia malayi. Parasitology 2014; 141:1341-52. [DOI: 10.1017/s0031182014000675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SUMMARYGuanylate kinase, a nucleoside monophosphate kinase of Brugia malayi which is involved in reversible transfer of phosphate groups from ATP to GMP, was cloned, expressed and characterized. The native molecular mass of BmGK was found to be 45 kDa as determined by size exclusion chromatography and glutaraldehyde cross-linking which revealed that the protein is homodimer in nature. This is a unique characteristic among known eukaryotic GKs. GMP and ATP served as the most effective phosphate acceptor and donor, respectively. Recombinant BmGK utilized both GMP and dGMP, as substrates showing Km values of 30 and 38 μm, respectively. Free Mg+2 (un-complexed to ATP) and GTP play a regulatory role in catalysis of BmGK. The enzyme showed higher catalytic efficiency as compared with human GK and showed ternary complex (BmGK-GMP-ATP) formation with sequential substrate binding. The secondary structure of BmGK consisted of 45% α-helices, 18% β-sheets as revealed by CD analysis. Homology modelling and docking with GMP revealed conserved substrate binding residues with slight differences. Differences in kinetic properties and oligomerization of BmGK compared with human GK can provide the way for design of parasite-specific inhibitors.
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Lin CY, Huang JY, Lo LW. Deciphering the catalysis-associated conformational changes of human adenylate kinase 1 with single-molecule spectroscopy. J Phys Chem B 2013; 117:13947-55. [PMID: 24134437 DOI: 10.1021/jp4019537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human adenylate kinase isoenzyme 1 (AK1) is the key enzyme in maintaining the cellular energy homeostasis. The catalysis-associated conformational changes of AK1 involve large-amplitude rearrangements. To decipher the conformational changes of AK1 at the single-molecule level, we tagged AK1 with two identical fluorophores, one near the substrate-binding site and the other at the boundary of the core domain. We found that magnesium ion binding to AK1 increases the structural heterogeneity of AK1, whereas ADP binding reduces the structural heterogeneity. We exploited the hidden Markov model to extract the underlying catalysis-associated conformational dynamics and determined thermodynamic parameters of the multiple catalytic pathways. The third-order correlation difference calculated from photon fluctuation traces reveals the irreversible nature of the conformational motions, suggesting that single-molecule AK1 is in a nonequilibrium steady state. This discovery offers a fresh viewpoint to look into the molecular mechanisms of cellular biochemistry.
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Affiliation(s)
- Chien Y Lin
- Department of Photonics, Chiao Tung University , Hsinchu, Taiwan
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Fujii A, Hirota S, Matsuo T. Reversible switching of fluorophore property based on intrinsic conformational transition of adenylate kinase during its catalytic cycle. Bioconjug Chem 2013; 24:1218-25. [PMID: 23718926 DOI: 10.1021/bc400160m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Adenylate kinase shows a conformational transition (OPEN and CLOSED forms) during substrate binding and product release to mediate the phosphoryl transfer between ADP and ATP/AMP. The protein motional characteristics will be useful to construct switching systems of fluorophore properties caused by the catalytic cycle of the enzyme. This paper demonstrates in situ reversible switching of a fluorophore property driven by the conformational transition of the enzyme. The pyrene-conjugated mutant adenylate kinase is able to switch the monomer/excimer emission property of pyrene on addition of ADP or P(1)P(5)-di(adenosine-5')pentaphosphate (Ap5A, a transition state analog). The observation under the dilute condition (~0.1 μM) indicates that the emission spectral change was caused by the motion of a protein molecule and not led by protein-protein interactions through π-π stacking of pyrene rings. The switching can be reversibly conducted by using hexokinase-coupling reaction. The fashion of the changes in emission intensities at various ligand concentrations is different between ADP, Mg(2+)-bound ADP, and Mg(2+)-bound Ap5A. The emission property switching is repeatable by a sequential addition of a substrate in a one-pot process. It is proposed that the property of a synthetic molecule on the enzyme surface is switchable in response to the catalytic cycle of adenylate kinase.
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Affiliation(s)
- Akira Fujii
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
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Meena LS, Dhakate SR, Sahare PD. Elucidation of Mg²⁺ binding activity of adenylate kinase from Mycobacterium tuberculosis H₃₇Rv using fluorescence studies. Biotechnol Appl Biochem 2012; 59:429-36. [PMID: 23586951 DOI: 10.1002/bab.1043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022]
Abstract
Adenylate kinase (AK) is a small ubiquitous enzyme that catalyzes the reversible transfer of the terminal phosphate group from adenine triphosphate (ATP): magnesium ion (Mg²⁺) to adenine monophosphate (AMP) to form two molecules of adenine diphosphate (ADP). AK thus maintains the homeostasis of adenine nucleotides in eukaryotes and prokaryotes. Because the [ATP]/[ADP] ratio is an important parameter in energy regulation in cells, Mg²⁺-activated AK has an important biological role, particularly in the case of bacteria, as imbalance in the ratio of [ATP]/[ADP] has been associated with alteration in its DNA supercoiling state. In the present study, magnesium-binding assays were carried out by systematically varying the concentrations of Mg²⁺, protein, AMP, ATP, and indicator in kinetic experiments. We report evidence that during magnesium-binding assay, the fluorescence level of the indicator "Mag-Indo-1" changes with protein concentration, suggesting that magnesium ions are binding to AK. The dual activity of AK both as nucleoside monophosphate and diphosphate kinases suggests that this enzyme may have a role in RNA and DNA biosynthesis in addition to its role in intracellular nucleotide metabolism. According to the proposed model, the magnesium-activated AK exhibits an increase in its forward reaction rate compared with the inactivated form. These findings imply that Mg²⁺ could be an important regulator in the energy signaling network in cells.
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Affiliation(s)
- Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India.
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Wang Y, Gan L, Wang E, Wang J. Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates. J Chem Theory Comput 2012; 9:84-95. [PMID: 26589012 DOI: 10.1021/ct300720s] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenylate kinase (ADK) has been explored widely, through both experimental and theoretical studies. However, still less is known about how the functional dynamics of ADK is modulated explicitly by its natural substrates. Here, we report a quantitative study of the dynamic energy landscape for ADK responding to the substrate binding by integrating both experimental investigations and theoretical modeling. We make theoretical predictions which are in remarkable agreement with the single molecule experiments on the substrate-bound complex. With our combined models of ADK in its apo form, in the presence of AMP or ATP, and in complex with both substrates, we specifically address the following key questions: (1) Are there intermediate state(s) during their catalytic cycle and if so how many? (2) How many pathways are there along the open-to-closed transitions and what are their corresponding weights? (3) How do substrates influence the pathway weights and the stability of the intermediates? (4) Which lid's motion is rate-limiting along the turnover cycle, the NMP or the LID domain? Our models predict two major parallel stepwise pathways and two on-pathway intermediates which are denoted as IN (NMP domain open while LID domain closed) and IL (LID domain open and NMP domain closed), respectively. Further investigation of temperature effects suggests that the IN pathway is dominant at room temperature, but the IL pathway is dominant at the optimal temperature. This leads us to propose that the IL pathway is more dominant by entropy and IN pathway by enthalpy. Remarkably, our results show that even with maximum concentrations of natural substrates, ADK still fluctuates between multiple functional states, reflecting an intrinsic capability of large-scale conformational fluctuations which may be essential to its biological function. The results based on the dual-ligands model provide the theoretical validation of random bisubstrate biproducts (Bi-Bi) mechanism for the enzymatic reaction of ADK. Additionally, the pathway flux analysis strongly suggests that the motion of the NMP domain is the rate-determining step for the conformational cycle (opening and closing).
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Linfeng Gan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China.,College of Physics, Jilin University, Changchun, Jilin, P.R. China.,Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, United States
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Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:076601. [PMID: 22790780 PMCID: PMC3695400 DOI: 10.1088/0034-4885/75/7/076601] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines. In this review, we discuss (1) the development of the energy landscape theory of biomolecular folding, (2) recent advances toward establishing a consistent understanding of folding and function and (3) emerging themes in the functional motions of enzymes, biomolecular motors and other biomolecular machines. Recent theoretical, computational and experimental lines of investigation have provided a very dynamic picture of biomolecular motion. In contrast to earlier ideas, where molecular machines were thought to function similarly to macroscopic machines, with rigid components that move along a few degrees of freedom in a deterministic fashion, biomolecular complexes are only marginally stable. Since the stabilizing contribution of each atomic interaction is on the order of the thermal fluctuations in solution, the rigid body description of molecular function must be revisited. An emerging theme is that functional motions encompass order-disorder transitions and structural flexibility provides significant contributions to the free energy. In this review, we describe the biological importance of order-disorder transitions and discuss the statistical-mechanical foundation of theoretical approaches that can characterize such transitions.
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Affiliation(s)
- Paul C Whitford
- Center for Theoretical Biological Physics, Department of Physics, Rice University, 6100 Main, Houston, TX 77005-1827, USA
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Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:189-98. [DOI: 10.1007/s00249-011-0772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 11/27/2022]
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Abstract
Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.
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Brokaw JB, Chu JW. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase. Biophys J 2011; 99:3420-9. [PMID: 21081091 DOI: 10.1016/j.bpj.2010.09.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 09/09/2010] [Accepted: 09/21/2010] [Indexed: 11/28/2022] Open
Abstract
We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro(177) on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro(177) hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.
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Affiliation(s)
- Jason B Brokaw
- Department of Chemistry, University of California, Berkeley, CA, USA
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Tan YW, Yang H. Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments. Phys Chem Chem Phys 2010; 13:1709-21. [PMID: 21183988 DOI: 10.1039/c0cp02412k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Enzymes are remarkable molecular machines that make many difficult biochemical reactions possible under mild biological conditions with incredible precision and efficiency. Our understanding of the working principles of enzymes, however, has not reached the level where one can readily deduce the mechanism and the catalytic rates from an enzyme's structure. Resolving the dynamics that relate the three-dimensional structure of an enzyme to its function has been identified as a key issue. While still challenging to implement, single-molecule techniques have emerged as one of the most useful methods for studying enzymes. We review enzymes studied using single-molecule fluorescent methods but placing them in the context of results from other complementary experimental work done on bulk samples. This review primarily covers three enzyme systems--flavoenzymes, dehydrofolate reductase, and adenylate kinase--with additional enzymes mentioned where appropriate. When the single-molecule experiments are discussed together with other methods aiming at the same scientific question, the weakness, strength, and unique contributions become clear.
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Affiliation(s)
- Yan-Wen Tan
- Department of Physics, Fudan University, No. 220, Handan Rd., Shanghai 200433, China.
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