1
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Zawistowski RK, Crane BR. Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature. J Mol Biol 2024; 436:168799. [PMID: 39332669 DOI: 10.1016/j.jmb.2024.168799] [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: 07/24/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 09/29/2024]
Abstract
In consideration of life in extreme environments, the effects of hydrostatic pressure on proteins at the atomic level have drawn substantial interest. Large deviations of temperature and pressure from ambient conditions can shift the free energy landscape of proteins to reveal otherwise lowly populated structural states and even promote unfolding. We report the crystal structure of the heme-containing peroxidase, cytochrome c peroxidase (CcP) at 1.5 and 3.0 kbar and make comparisons to structures determined at 1.0 bar and cryo-temperatures (100 K). Pressure produces anisotropic changes in CcP, but compressibility plateaus after 1.5 kbar. CcP responds to pressure with volume declines at the periphery of the protein where B-factors are relatively high but maintains nearly intransient core structure, hydrogen bonding interactions and active site channels. Changes in active-site solvation and heme ligation reveal pressure sensitivity to protein-ligand interactions and a potential docking site for the substrate peroxide. Compression at the surface affects neither alternate side-chain conformers nor B-factors. Thus, packing in the core, which resembles a crystalline solid, limits motion and protects the active site, whereas looser packing at the surface preserves side-chain dynamics. These data demonstrate that conformational dynamics and packing densities are not fully correlated in proteins and that encapsulation of cofactors by the polypeptide can provide a precisely structured environment resistant to change across a wide range of physical conditions.
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Affiliation(s)
- Rebecca K Zawistowski
- Department of Chemistry and Chemical Biology, Cornell University, 122 Baker Laboratory, Ithaca, NY 14853, USA.
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, 122 Baker Laboratory, Ithaca, NY 14853, USA.
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2
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Lin YW. Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions. J Inorg Biochem 2024; 257:112595. [PMID: 38759262 DOI: 10.1016/j.jinorgbio.2024.112595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China.
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3
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Chen ZY, Yuan H, Wang H, Sun LJ, Yu L, Gao SQ, Tan X, Lin YW. Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin. Chembiochem 2024; 25:e202300678. [PMID: 38015421 DOI: 10.1002/cbic.202300678] [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: 10/03/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 11/29/2023]
Abstract
Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.
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Affiliation(s)
- Ze-Yuan Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
- Hengyang Medical School, University of South China, Hengyang, 421001, China
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4
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [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: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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5
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Sharma S, Skaist Mehlman T, Sagabala RS, Boivin B, Keedy DA. High-resolution double vision of the allosteric phosphatase PTP1B. Acta Crystallogr F Struct Biol Commun 2024; 80:1-12. [PMID: 38133579 PMCID: PMC10833341 DOI: 10.1107/s2053230x23010749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.
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Affiliation(s)
- Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- PhD Program in Biology, CUNY Graduate Center, New York, NY 10016, USA
| | - Tamar Skaist Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Reddy Sudheer Sagabala
- Department of Nanobioscience, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Benoit Boivin
- Department of Nanobioscience, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology and Chemistry, CUNY Graduate Center, New York, NY 10016, USA
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6
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Colloc'h N, Dhaussy AC, Girard E. Exploring the structural dynamics of proteins by pressure perturbation using macromolecular crystallography. Methods Enzymol 2023; 688:349-381. [PMID: 37748831 DOI: 10.1016/bs.mie.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
High pressure is a convenient thermodynamic parameter to probe the dynamics of proteins as it is intimately related to volume which is essential for protein function. To be biologically active, a protein fluctuates between different substates. Pressure perturbation can promote some hidden substates by modifying the population between them. High pressure macromolecular crystallography (HPMX) is a perfect tool to capture and to characterize such substates at a molecular level providing new insights on protein dynamics. The present chapter describes the use of the diamond anvil cell to perform HPMX experiments. It also provides tips on sample preparation and optimal data collection as well as on efficient analysis of the resulting high-pressure structures.
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Affiliation(s)
- Nathalie Colloc'h
- Imagerie et stratégies thérapeutiques pour les cancers et tissus cérébraux (ISTCT), CNRS Université de Caen Normandie, Centre Cyceron, Caen, France
| | | | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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7
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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8
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Sun LJ, Yuan H, Xu JK, Luo J, Lang JJ, Wen GB, Tan X, Lin YW. Phenoxazinone Synthase-like Activity of Rationally Designed Heme Enzymes Based on Myoglobin. Biochemistry 2023; 62:369-377. [PMID: 34665595 DOI: 10.1021/acs.biochem.1c00554] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The design of functional metalloenzymes is attractive for the biosynthesis of biologically important compounds, such as phenoxazinones and phenazines catalyzed by native phenoxazinone synthase (PHS). To design functional heme enzymes, we used myoglobin (Mb) as a model protein and introduced an artificial CXXC motif into the heme distal pocket by F46C and L49C mutations, which forms a de novo disulfide bond, as confirmed by the X-ray crystal structure. We further introduced a catalytic Tyr43 into the heme distal pocket and found that the F43Y/F46C/L49C Mb triple mutant and the previously designed F43Y/F46S Mb exhibit PHS-like activity (80-98% yields in 5-15 min), with the catalytic efficiency exceeding those of natural metalloenzymes, including o-aminophenol oxidase, laccase, and dye-decolorizing peroxidase. Moreover, we showed that the oxidative coupling product of 1,6-disulfonic-2,7-diaminophenazine is a potential pH indicator, with the orange-magenta color change at pH 4-5 (pKa = 4.40). Therefore, this study indicates that functional heme enzymes can be rationally designed by structural modifications of Mb, exhibiting the functionality of the native PHS for green biosynthesis.
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Affiliation(s)
- Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jie Luo
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Jia-Jia Lang
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- Hengyang Medical School, University of South China, Hengyang 421001, China.,Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
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9
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Efficient Degradation of Tetracycline Antibiotics by Engineered Myoglobin with High Peroxidase Activity. Molecules 2022; 27:molecules27248660. [PMID: 36557794 PMCID: PMC9782475 DOI: 10.3390/molecules27248660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Tetracyclines are one class of widely used antibiotics. Meanwhile, due to abuse and improper disposal, they are often detected in wastewater, which causes a series of environmental problems and poses a threat to human health and safety. As an efficient and environmentally friendly method, enzymatic catalysis has attracted much attention. In previous studies, we have designed an efficient peroxidase (F43Y/P88W/F138W Mb, termed YWW Mb) based on the protein scaffold of myoglobin (Mb), an O2 carrier, by modifying the heme active center and introducing two Trp residues. In this study, we further applied it to degrade the tetracycline antibiotics. Both UV-Vis and HPLC studies showed that the triple mutant YWW Mb was able to catalyze the degradation of tetracycline, oxytetracycline, doxycycline, and chlortetracycline effectively, with a degradation rate of ~100%, ~98%, ~94%, and ~90%, respectively, within 5 min by using H2O2 as an oxidant. These activities are much higher than those of wild-type Mb and other heme enzymes such as manganese peroxidase. As further analyzed by UPLC-ESI-MS, we identified multiple degradation products and thus proposed possible degradation mechanisms. In addition, the toxicity of the products was analyzed by using in vitro antibacterial experiments of E. coli. Therefore, this study indicates that the engineered heme enzyme has potential applications for environmental remediation by degradation of tetracycline antibiotics.
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10
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Sun LJ, Yuan H, Yu L, Gao SQ, Wen GB, Tan X, Lin YW. Structural and functional regulations by a disulfide bond designed in myoglobin like human neuroglobin. Chem Commun (Camb) 2022; 58:5885-5888. [PMID: 35471205 DOI: 10.1039/d2cc01753a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An artificial disulfide bond (Cys46-Cys61) was designed in the heme distal site of myoglobin, which regulates the conformation of the heme distal His64 and the protein reactivity, as confirmed by X-ray crystallography, EPR, and kinetic UV-vis studies. This study shows the successful design of a disulfide bond with suitable positions in globins, conferring a structure and function like those of the native human neuroglobin.
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Affiliation(s)
- Li-Juan Sun
- Hengyang Medical College, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shu-Qin Gao
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- Hengyang Medical College, University of South China, Hengyang 421001, China. .,Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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11
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Seelig J, Seelig A. Molecular understanding of calorimetric protein unfolding experiments. BIOPHYSICAL REPORTS 2022; 2:100037. [PMID: 36425081 PMCID: PMC9680786 DOI: 10.1016/j.bpr.2021.100037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/02/2021] [Indexed: 06/16/2023]
Abstract
Testing and predicting protein stability gained importance because proteins, including antibodies, became pharmacologically relevant in viral and cancer therapies. Isothermal scanning calorimetry is the principle method to study protein stability. Here, we use the excellent experimental heat capacity Cp(T) data from the literature for a critical inspection of protein unfolding as well as for the test of a new cooperative model. In the relevant literature, experimental temperature profiles of enthalpy, Hcal(T), entropy, Scal(T), and free energy, Gcal(T) are missing. First, we therefore calculate the experimental Hcal(T), Scal(T), and Gcal(T) from published Cp(T) thermograms. Considering only the unfolding transition proper, the heat capacity and all thermodynamic functions are zero in the region of the native protein. In particular, the free energy of the folded proteins is also zero and Gcal(T) displays a trapezoidal temperature profile when cold denaturation is included. Second, we simulate the DSC-measured thermodynamic properties with a new molecular model based on statistical-mechanical thermodynamics. The model quantifies the protein cooperativity and predicts the aggregate thermodynamic variables of the system with molecular parameters only. The new model provides a perfect simulation of all thermodynamic properties, including the observed trapezoidal Gcal(T) temperature profile. Importantly, the new cooperative model can be applied to a broad range of protein sizes, including antibodies. It predicts not only heat and cold denaturation but also provides estimates of the unfolding kinetics and allows a comparison with molecular dynamics calculations and quasielastic neutron scattering experiments.
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Affiliation(s)
| | - Anna Seelig
- Biozentrum, University of Basel, Basel, Switzerland
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12
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Gao SQ, Yuan H, Yang XZ, Xiang HF, Tan X, Wen GB, Lin YW. Improving the cell-membrane-penetrating activity of globins by introducing positive charges on protein surface: A case study of sperm whale myoglobin. Biochem Biophys Res Commun 2022; 598:26-31. [PMID: 35151200 DOI: 10.1016/j.bbrc.2022.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022]
Abstract
Globins are heme proteins such as hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb), playing important roles in biological system. In addition to normal functions, zebrafish Ngb was able to penetrate cell membranes, whereas less was known for other globin members. In this study, to improve the cell-membrane-penetrating activity of globins, we used sperm whale Mb as a model protein and constructed a quadruple mutant of G5K/Q8K/A19K/V21K Mb (termed 4K Mb), by introduction of four positive charges on the protein surface, which was designed according to the amino acid alignment with that of zebrafish Ngb. Spectroscopic and crystallographic studies showed that the four positively charged Lys residues did not affect the protein structure. Cell-membrane-penetrating essay further showed that 4K Mb exhibited enhanced activity compared to that of native Mb. This study provides valuable information for the effect of distribution of charged residues on the protein structure and the cell-membrane-penetrating activity of globins. Therefore, it will guide the design of protein-based biomaterials for biological applications.
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Affiliation(s)
- Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Xin-Zhi Yang
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Heng-Fang Xiang
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ge-Bo Wen
- Hengyang Medical School, University of South China, Hengyang, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China.
| | - Ying-Wu Lin
- Hengyang Medical School, University of South China, Hengyang, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, 421001, China.
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13
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Liu J, Xu JK, Yuan H, Wang XJ, Gao SQ, Wen GB, Tan XS, Lin YW. Engineering globins for efficient biodegradation of malachite green: two case studies of myoglobin and neuroglobin. RSC Adv 2022; 12:18654-18660. [PMID: 35873322 PMCID: PMC9229271 DOI: 10.1039/d2ra02795j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022] Open
Abstract
Engineered globins such as H64D Mb and A15C/H64D Ngb were efficient in the degradation of malachite green, with activities much higher than those of some native enzymes.
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Affiliation(s)
- Jiao Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Hong Yuan
- Department of Chemistry, Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiang-Shi Tan
- Department of Chemistry, Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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14
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Guo WJ, Xu JK, Wu ST, Gao SQ, Wen GB, Tan X, Lin YW. Design and Engineering of an Efficient Peroxidase Using Myoglobin for Dye Decolorization and Lignin Bioconversion. Int J Mol Sci 2021; 23:ijms23010413. [PMID: 35008837 PMCID: PMC8745427 DOI: 10.3390/ijms23010413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
The treatment of environmental pollutants such as synthetic dyes and lignin has received much attention, especially for biotechnological treatments using both native and artificial metalloenzymes. In this study, we designed and engineered an efficient peroxidase using the O2 carrier myoglobin (Mb) as a protein scaffold by four mutations (F43Y/T67R/P88W/F138W), which combines the key structural features of natural peroxidases such as the presence of a conserved His-Arg pair and Tyr/Trp residues close to the heme active center. Kinetic studies revealed that the quadruple mutant exhibits considerably enhanced peroxidase activity, with the catalytic efficiency (kcat/Km) comparable to that of the most efficient natural enzyme, horseradish peroxidase (HRP). Moreover, the designed enzyme can effectively decolorize a variety of synthetic organic dyes and catalyze the bioconversion of lignin, such as Kraft lignin and a model compound, guaiacylglycerol-β-guaiacyl ether (GGE). As analyzed by HPLC and ESI-MS, we identified several bioconversion products of GGE, as produced via bond cleavage followed by dimerization or trimerization, which illustrates the mechanism for lignin bioconversion. This study indicates that the designed enzyme could be exploited for the decolorization of textile wastewater contaminated with various dyes, as well as for the bioconversion of lignin to produce more value-added products.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Jia-Kun Xu
- Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China;
| | - Sheng-Tao Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Shu-Qin Gao
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Ge-Bo Wen
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China;
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
- Correspondence: ; Tel.: +86-734-8282375
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15
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Eltareb A, Lopez GE, Giovambattista N. The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine. Phys Chem Chem Phys 2021; 23:19402-19414. [PMID: 34494044 PMCID: PMC8491127 DOI: 10.1039/d1cp02734d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures (T ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water can exist in two amorphous ices at P < 1 GPa, low-density amorphous (LDA) ice at low pressures and high-density amorphous ice (HDA) at high pressures; HDA is ≈20-25% denser than LDA. While fast/plunge cooling at 1 bar brings the sample into LDA, high-pressure cooling (HPC), at sufficiently high pressure, produces HDA. HDA can also be produced by isothermal compression of LDA at cryogenic temperatures. Here, we perform classical molecular dynamics simulations to study the effects of LDA, HDA, and the LDA-HDA transformation on the structure and hydration of a small peptide, polyalanine. We follow thermodynamic paths corresponding to (i) fast/plunge cooling at 1 bar, (ii) HPC at P = 400 MPa, and (iii) compression/decompression cycles at T = 80 K. While process (i) produced LDA in the system, path (iii) produces HDA. Interestingly, the amorphous ice produced in process (ii) is an intermediate amorphous ice (IA) with properties that fall in-between those of LDA and HDA. Remarkably, the structural changes in polyalanine are negligible at all conditions studied (0-2000 MPa, 80-300 K) even when water changes among the low and high-density liquid states as well as the amorphous solids LDA, IA, and HDA. The similarities and differences in the hydration of polyalanine vitrified in LDA, IA, and HDA are described. Since the studied thermodynamic paths are suitable for the cryopreservation of biomolecules, we also study the structure and hydration of polyalanine along isobaric and isochoric heating paths, which can be followed experimentally for the recovery of cryopreserved samples. Upon heating, the structure of polyalanine remains practically unchanged. We conclude with a brief discussion of the practical advantages of (a) using HDA and IA as a cryoprotectant environment (as opposed to LDA), and (b) the use of isochoric heating as a recovery process (as opposed to isobaric heating).
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Affiliation(s)
- Ali Eltareb
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Gustavo E Lopez
- Department of Chemistry, Lehman College of the City University of New York, Bronx, New York 10468, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Nicolas Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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16
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Guo WJ, Xu JK, Liu JJ, Lang JJ, Gao SQ, Wen GB, Lin YW. Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group. Front Bioeng Biotechnol 2021; 9:664388. [PMID: 34136471 PMCID: PMC8201792 DOI: 10.3389/fbioe.2021.664388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao, China
| | - Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Jia Lang
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
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17
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Xiang HF, Xu JK, Liu J, Yang XZ, Gao SQ, Wen GB, Lin YW. Efficient biodegradation of malachite green by an artificial enzyme designed in myoglobin. RSC Adv 2021; 11:16090-16095. [PMID: 35481174 PMCID: PMC9029994 DOI: 10.1039/d1ra02202d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/25/2021] [Indexed: 12/26/2022] Open
Abstract
Synthetic dyes such as malachite green (MG) have a wide range of applications. Meanwhile, they bring great challenges for environmental security and cause potential damages to human health. Compared with traditional approaches, enzymatic catalysis is an emerging technique for wastewater treatment. As alternatives to natural enzymes, artificial enzymes have received much attention for potential applications. In previous studies, we have rationally designed artificial enzymes based on myoglobin (Mb), such as by introducing a distal histidine (F43H mutation) and creating a channel to the heme pocket (H64A mutation). We herein show that the artificial enzyme of F43H/H64A Mb can be successfully applied for efficient biodegradation of MG under weak acid conditions. The degradation efficiency is much higher than those of natural enzymes, such as dye-decolorizing peroxidase and laccase (13-18-fold). The interaction of MG and F43H/H64A Mb was investigated by using both experimental and molecular docking studies, and the biodegradation products of MG were also revealed by UPLC-ESI-MS analysis. Based on these results, we proposed a plausible biodegradation mechanism of MG. With the high-yield of overexpression in E. coli cells, this study suggests that the artificial enzyme has potential applications in the biodegradation of MG in fisheries and textile industries.
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Affiliation(s)
- Heng-Fang Xiang
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology Qingdao 266071 China
| | - Jiao Liu
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
| | - Xin-Zhi Yang
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China Hengyang 421001 China
- Laboratory of Protein Structure and Function, University of South China Medical School Hengyang 421001 China
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18
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Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Nat Commun 2021; 12:1672. [PMID: 33723266 PMCID: PMC7960726 DOI: 10.1038/s41467-021-21819-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.
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Affiliation(s)
- Marie Luise Grünbein
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Alexander Gorel
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Lutz Foucar
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sergio Carbajo
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - William Colocho
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sasha Gilevich
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Elisabeth Hartmann
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mario Hilpert
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mark Hunter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Marco Kloos
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.434729.f0000 0004 0590 2900Present Address: European XFEL GmbH, Schenefeld, Germany
| | - Jason E. Koglin
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.148313.c0000 0004 0428 3079Present Address: Los Alamos National Laboratory, Los Alamos, NM USA
| | - Thomas J. Lane
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.466493.a0000 0004 0390 1787Present Address: Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Jim Lewandowski
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Alberto Lutman
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Karol Nass
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.5991.40000 0001 1090 7501Present Address: Paul Scherrer Institut, Villigen, Switzerland
| | - Gabriela Nass Kovacs
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Christopher M. Roome
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - John Sheppard
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Robert L. Shoeman
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Miriam Stricker
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.4991.50000 0004 1936 8948Present Address: Department of Statistics, University of Oxford, Oxford, UK
| | - Tim van Driel
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sharon Vetter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - R. Bruce Doak
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sébastien Boutet
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Andrew Aquila
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Franz Josef Decker
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Thomas R. M. Barends
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Claudiu Andrei Stan
- grid.430387.b0000 0004 1936 8796Department of Physics, Rutgers University Newark, Newark, NJ USA
| | - Ilme Schlichting
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
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19
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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20
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Rational Design of an Artificial Nuclease by Engineering a Hetero-Dinuclear Center of Mg-Heme in Myoglobin. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04572] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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McMonagle CJ, Allan DR, Warren MR, Kamenev KV, Turner GF, Moggach SA. High-pressure sapphire capillary cell for synchrotron single-crystal X-ray diffraction measurements to 1500 bar. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720013710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new sapphire capillary pressure cell for single-crystal X-ray diffraction measurements at moderate pressures (200−1500 bar; 1 bar = 100 kPa) has been developed and optimized for use on beamline I19 at Diamond Light Source. The three-component cell permits optical centring of the crystal and in situ pressure modification to a precision of 1 bar. Compression of hexamethylenetetramine and its deuterated analogue to 1000 bar was performed, showcasing the accuracy and precision of the measurements, and highlighting evidence of a geometric isotope effect.
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22
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Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond. Int J Mol Sci 2020; 21:ijms21072512. [PMID: 32260401 PMCID: PMC7177771 DOI: 10.3390/ijms21072512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/23/2022] Open
Abstract
Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.
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23
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Helliwell JR. What is the structural chemistry of the living organism at its temperature and pressure? Acta Crystallogr D Struct Biol 2020; 76:87-93. [PMID: 32038039 PMCID: PMC7008516 DOI: 10.1107/s2059798320000546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/02/2022] Open
Abstract
The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature will never be performed at room temperature, crystallization often requires nonphysiological chemical conditions, and X-rays and electrons cause beam damage. However, integrated structural biology techniques and functional assays provide a package towards physiological relevance of any given study. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are, as discussed in detail in this feature article.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, England
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24
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Zhang P, Yuan H, Xu J, Wang XJ, Gao SQ, Tan X, Lin YW. A Catalytic Binding Site Together with a Distal Tyr in Myoglobin Affords Catalytic Efficiencies Similar to Natural Peroxidases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b05080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ping Zhang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
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25
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Zhang P, Xu J, Wang XJ, He B, Gao SQ, Lin YW. The Third Generation of Artificial Dye-Decolorizing Peroxidase Rationally Designed in Myoglobin. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02226] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ping Zhang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
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26
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Lin Y. Rational design of heme enzymes for biodegradation of pollutants toward a green future. Biotechnol Appl Biochem 2019; 67:484-494. [DOI: 10.1002/bab.1788] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang People's Republic of China
- Laboratory of Protein Structure and Function University of South China Hengyang People's Republic of China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang People's Republic of China
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27
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Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallogr D Struct Biol 2019; 75:123-137. [PMID: 30821702 PMCID: PMC6400254 DOI: 10.1107/s2059798318017941] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023] Open
Abstract
Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at different sites in a protein structure and to estimate the degree of energetic coupling between them is discussed. These insights can suggest testable hypotheses about allosteric mechanisms. Temperature is an easily manipulated experimental parameter, so the MMX approach is widely applicable to any protein that yields well diffracting crystals. Moreover, the general principles of MMX are extensible to other perturbations such as pH, pressure, ligand concentration etc. Future work will explore strategies for leveraging X-ray data across such perturbation series to more quantitatively measure how different parts of a protein structure are coupled to each other, and the consequences thereof for allostery and other aspects of protein function.
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Affiliation(s)
- Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, USA
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Mass Spectrometry- and Computational Structural Biology-Based Investigation of Proteins and Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:265-287. [PMID: 31347053 DOI: 10.1007/978-3-030-15950-4_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent developments of mass spectrometry (MS) allow us to identify, estimate, and characterize proteins and protein complexes. At the same time, structural biology helps to determine the protein structure and its structure-function relationship. Together, they aid to understand the protein structure, property, function, protein-complex assembly, protein-protein interaction, and dynamics. The present chapter is organized with illustrative results to demonstrate how experimental mass spectrometry can be combined with computational structural biology for detailed studies of protein's structures. We have used tumor differentiation factor protein/peptide as ligand and Hsp70/Hsp90 as receptor protein as examples to study ligand-protein interaction. To investigate possible protein conformation, we will describe two proteins-lysozyme and myoglobin. As an application of MS-based assignment of disulfide bridges, the case of the spider venom polypeptide Phα1β will also be discussed.
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Liu HX, Li L, He B, Gao SQ, Wen GB, Lin YW. Neuroglobin is capable of self-oxidation of methionine64 introduced at the heme axial position. Dalton Trans 2018; 47:10847-10852. [PMID: 30027178 DOI: 10.1039/c8dt02397b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Neuroglobin (Ngb), with its physiological role not fully understood, was found to be capable of self-oxidation of methionine64 introduced at the heme axial position (H64M Ngb), adopting a high-spin heme state and producing both methionine sulfoxide (SO-Met) and sulfone (SO2-Met), which represents the structure and function of cytochrome c in a non-native state.
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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30
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Yin L, Yuan H, Liu C, He B, Gao SQ, Wen GB, Tan X, Lin YW. A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02979] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu−Lu Yin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Can Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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31
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Cheng HM, Yuan H, Wang XJ, Xu JK, Gao SQ, Wen GB, Tan X, Lin YW. Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen. J Inorg Biochem 2018; 182:141-149. [PMID: 29477977 DOI: 10.1016/j.jinorgbio.2018.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O2, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H2O2. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.
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Affiliation(s)
- Hui-Min Cheng
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Yellow Sea Fisheries Research Institute, Qingdao 266071, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Lab of Protein Structure and Function, University of South China, Hengyang 421001, China.
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32
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Yin LL, Yuan H, Du KJ, He B, Gao SQ, Wen GB, Tan X, Lin YW. Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin. Chem Commun (Camb) 2018; 54:4356-4359. [DOI: 10.1039/c8cc01646a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.
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Affiliation(s)
- Lu-Lu Yin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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33
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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34
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Li LL, Yuan H, Liao F, He B, Gao SQ, Wen GB, Tan X, Lin YW. Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center. Dalton Trans 2017; 46:11230-11238. [DOI: 10.1039/c7dt02302b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial dye-decolorizing peroxidases (DyPs) have been rationally designed using myoglobin (Mb) as a protein scaffold by engineering Tyr/Trp in the heme center, such as F43Y/F138 W Mb, which exhibited catalytic performance comparable to some native DyPs.
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Affiliation(s)
- Le-Le Li
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Fei Liao
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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35
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Espinosa YR, Grigera JR, Caffarena ER. Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin. Proteins 2017; 85:125-136. [PMID: 27802581 DOI: 10.1002/prot.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Abstract
The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high-pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125-136. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yanis R Espinosa
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - J Raúl Grigera
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
- Departmento de Biología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Ernesto R Caffarena
- Fundação Oswaldo Cruz., Rio de Janeiro, Programa de Computação Científica (PROCC), CEP, 21040-360, Rio de Janeiro, Brazil
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36
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Wu LB, Du KJ, Nie CM, Gao SQ, Wen GB, Tan X, Lin YW. Peroxidase activity enhancement of myoglobin by two cooperative distal histidines and a channel to the heme pocket. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Liao F, Yuan H, Du KJ, You Y, Gao SQ, Wen GB, Lin YW, Tan X. Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin. MOLECULAR BIOSYSTEMS 2016; 12:3139-45. [PMID: 27476534 DOI: 10.1039/c6mb00537c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.
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Affiliation(s)
- Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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38
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Wu LB, Yuan H, Zhou H, Gao SQ, Nie CM, Tan X, Wen GB, Lin YW. An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity. Arch Biochem Biophys 2016; 600:47-55. [DOI: 10.1016/j.abb.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 01/08/2023]
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39
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Shu X, Su J, Du K, You Y, Gao S, Wen G, Tan X, Lin Y. Rational Design of Dual Active Sites in a Single Protein Scaffold: A Case Study of Heme Protein in Myoglobin. ChemistryOpen 2016; 5:192-196. [PMID: 27933225 PMCID: PMC5125789 DOI: 10.1002/open.201500224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/03/2023] Open
Abstract
Rational protein design has been proven to be a powerful tool for creating functional artificial proteins. Although many artificial metalloproteins with a single active site have been successfully created, those with dual active sites in a single protein scaffold are still relatively rare. In this study, we rationally designed dual active sites in a single heme protein scaffold, myoglobin (Mb), by retaining the native heme site and creating a copper-binding site remotely through a single mutation of Arg118 to His or Met. Isothermal titration calorimetry (ITC) and electron paramagnetic resonance (EPR) studies confirmed that a copper-binding site of [3-His] or [2-His-1-Met] motif was successfully created in the single mutant of R118H Mb and R118M Mb, respectively. UV/Vis kinetic spectroscopy and EPR studies further revealed that both the heme site and the designed copper site exhibited nitrite reductase activity. This study presents a new example for rational protein design with multiple active sites in a single protein scaffold, which also lays the groundwork for further investigation of the structure and function relationship of heme/non-heme proteins.
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Affiliation(s)
- Xiao‐Gang Shu
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Ji‐Hu Su
- Department of Modern PhysicsUniversity of Science and Technology of ChinaHefei230026P. R. China
| | - Ke‐Jie Du
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Yong You
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Shu‐Qin Gao
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Ge‐Bo Wen
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Xiangshi Tan
- Department of ChemistryShanghai Key Lab of Chemical Biology for Protein Research& Institute of Biomedical ScienceFudan UniversityShanghai200433P. R. China
| | - Ying‐Wu Lin
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
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Wu LB, Yuan H, Gao SQ, You Y, Nie CM, Wen GB, Lin YW, Tan X. Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center. Nitric Oxide 2016; 57:21-29. [PMID: 27108710 DOI: 10.1016/j.niox.2016.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Heme proteins perform diverse functions in living systems, of which nitrite reductase (NIR) activity receives much attention recently. In this study, to better understand the structural elements responsible for the NIR activity, we used myoglobin (Mb) as a model heme protein and redesigned the heme active center, by introducing one or two distal histidines, and by creating a channel to the heme center with removal of the native distal His64 gate (His to Ala mutation). UV-Vis kinetic studies, combined with EPR studies, showed that a single distal histidine with a suitable position to the heme iron, i.e., His43, is crucial for nitrite (NO2(-)) to nitric oxide (NO) reduction. Moreover, creation of a water channel to the heme center significantly enhanced the NIR activity compared to the corresponding mutant without the channel. In addition, X-ray crystallographic studies of F43H/H64A Mb and its complexes with NO2(-) or NO revealed a unique hydrogen-bonding network in the heme active center, as well as unique substrate and product binding models, providing valuable structural information for the enhanced NIR activity. These findings enriched our understanding of the structure and NIR activity relationship of heme proteins. The approach of creating a channel in this study is also useful for rational design of other functional heme proteins.
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Affiliation(s)
- Lei-Bin Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Yong You
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
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Zhao Y, Du KJ, Gao SQ, He B, Wen GB, Tan X, Lin YW. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center. J Inorg Biochem 2016; 156:113-21. [DOI: 10.1016/j.jinorgbio.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 12/14/2022]
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43
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Classic Analysis of Biopolymer Dynamics Is Model Free. Biophys J 2016; 110:3-6. [PMID: 26745403 DOI: 10.1016/j.bpj.2015.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/02/2015] [Accepted: 11/16/2015] [Indexed: 11/21/2022] Open
Abstract
Early analysis of biopolymer dynamics relied on a variety of motional models that were difficult to distinguish and sometimes gave contradictory results. The Lipari-Szabo model-free approach (documented in a 1980 article in Biophysical Journal, as well as in two more comprehensive 1982 articles in the Journal of the American Chemical Society, provided a simple formalism that allowed investigators to understand fluorescence and NMR experimental data without having to specify a motional model. Although the model-free method is not universally applicable (for example, its assumption of a uniform correlation time for overall molecular tumbling can be problematic for biomolecules containing areas of disorder), it remains the most popular and widely used technique for analyzing molecular motion.
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High-Pressure EPR and Site-Directed Spin Labeling for Mapping Molecular Flexibility in Proteins. Methods Enzymol 2015; 564:29-57. [PMID: 26477247 DOI: 10.1016/bs.mie.2015.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
High hydrostatic pressure is a powerful probe of protein conformational flexibility. Pressurization reveals regions of elevated compressibility, and thus flexibility, within individual conformational states, but also shifts conformational equilibria such that "invisible" excited states become accessible for spectroscopic characterization. The central aim of this chapter is to describe recently developed instrumentation and methodologies that enable high-pressure site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) experiments on proteins and to demonstrate the information content of these experiments by highlighting specific recent applications. A brief introduction to the thermodynamics of proteins under pressure is presented first, followed by a discussion of the principles underlying SDSL-EPR detection of pressure effects in proteins, and the suitability of SDSL-EPR for this purpose in terms of timescale and ability to characterize conformational heterogeneity. Instrumentation and practical considerations for variable-pressure continuous wave EPR and pressure-resolved double electron-electron resonance (PR DEER) experiments are reviewed, and finally illustrations of data analysis using recent applications are presented. Although high-pressure SDSL-EPR is in its infancy, the recent applications presented highlight the considerable potential of the method to (1) identify compressible (flexible) regions in a folded protein; (2) determine thermodynamic parameters that relate conformational states in equilibrium; (3) populate and characterize excited states of proteins undetected at atmospheric pressure; (4) reveal the structural heterogeneity of conformational ensembles and provide distance constraints on the global structure of pressure-populated states with PR DEER.
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Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
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Fast-folding proteins under stress. Cell Mol Life Sci 2015; 72:4273-85. [PMID: 26231095 DOI: 10.1007/s00018-015-2002-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/07/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Proteins are subject to a variety of stresses in biological organisms, including pressure and temperature, which are the easiest stresses to simulate by molecular dynamics. We discuss the effect of pressure and thermal stress on very-fast-folding model proteins, whose in vitro folding can be fully simulated on computers and compared with experiments. We then discuss experiments that can be used to subject proteins to low- and high-temperature unfolding, as well as low- and high-pressure unfolding. Pressure and temperature are prototypical perturbations that illustrate how close many proteins are to instability, a property that cells can exploit to control protein function. We conclude by reviewing some recent in-cell experiments, and progress being made in simulating and measuring protein stability and function inside live cells.
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Abstract
At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.
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High Pressure Macromolecular Crystallography. Subcell Biochem 2015. [PMID: 26174404 DOI: 10.1007/978-94-017-9918-8_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
X-ray crystallography is a powerful tool for the high resolution structural study of biomacromolecules. One of the most important beneficial feature of the method is the possibility of the direct observation of hydration water structure. In recent years, significant development in high-pressure macromolecular crystallography (HPMX) using a diamond anvil cell (DAC) has been performed in combination with shorter wavelength X-ray of synchrotron radiation. The number of protein structures determined by HPMX at pressure ranging from several hundred MPa to 1 GPa is gradually growing. In this chapter, we describe DAC with its usage, and then an example of HPMX study on hydration structure of 3-isopropylmalate dehydrogenase (IPMDH).
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Abstract
In the last few years, advances in algal research have identified the participation of haemoglobins in nitrogen metabolism and the management of reactive nitrogen and oxygen species. This chapter summarises the state of knowledge concerning algal haemoglobins with a focus on the most widely used model system, namely, Chlamydomonas reinhardtii. Genetic, physiologic, structural, and chemical information is compiled to provide a framework for further studies.
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Affiliation(s)
- Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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Abstract
Hydrostatic pressure leads to nonuniform compression of proteins. The structural change is on average only about 0.1 Å kbar(-1), and is therefore within the range of fluctuations at ambient pressure. The largest changes are around cavities and buried water molecules. Sheets distort much more than helices. Hydrogen bonds compress about 0.012 Å kbar(-1), although there is a wide range, including some hydrogen bonds that lengthen. In the presence of ligands and inhibitors, structural changes are smaller. Pressure has little effect on rapid fluctuations, but with larger scale slower motions, pressure increases the population of excited states (if they have smaller overall volume), and slows the fluctuations. In barnase, pressure is shown to be a useful way to characterise fluctuations on the timescale of microseconds, and helps to show that fluctuations in barnase are hierarchical, with the faster fluctuations providing a platform for the slower ones. The excited states populated at high pressure are probably functionally important.
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Affiliation(s)
- Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK,
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