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Ohler A, Taylor PE, Bledsoe JA, Iavarone AT, Gilbert NC, Offenbacher AR. Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers. ACS Catal 2024; 14:5444-5457. [PMID: 38601784 PMCID: PMC11003420 DOI: 10.1021/acscatal.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The oxidation of polyunsaturated fatty acids by lipoxygenases (LOXs) is initiated by a C-H cleavage step in which the hydrogen atom is transferred quantum mechanically (i.e., via tunneling). In these reactions, protein thermal motions facilitate the conversion of ground-state enzyme-substrate complexes to tunneling-ready configurations and are thus important for transferring energy from the solvent to the active site for the activation of catalysis. In this report, we employed temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX-MS) to identify catalytically linked, thermally activated peptides in a representative animal LOX, human epithelial 15-LOX-2. TDHDX-MS of wild-type 15-LOX-2 was compared to two active site mutations that retain structural stability but have increased activation energies (Ea) of catalysis. The Ea value of one variant, V427L, is implicated to arise from suboptimal substrate positioning by increased active-site side chain rotamer dynamics, as determined by X-ray crystallography and ensemble refinement. The resolved thermal network from the comparative Eas of TDHDX-MS between wild-type and V426A is localized along the front face of the 15-LOX-2 catalytic domain. The network contains a clustering of isoleucine, leucine, and valine side chains within the helical peptides. This thermal network of 15-LOX-2 is different in location, area, and backbone structure compared to a model plant lipoxygenase from soybean that exhibits a low Ea value of catalysis compared to the human ortholog. The presented data provide insights into the divergence of thermally activated protein motions in plant and animal LOXs and their relationships to the enthalpic barriers for facilitating hydrogen tunneling.
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Affiliation(s)
- Amanda Ohler
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Paris E. Taylor
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Jasmine A. Bledsoe
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Anthony T. Iavarone
- QB3/Chemistry
Mass Spectrometry Facility, University of
California, Berkeley, Berkeley, California 94720, United States
| | - Nathaniel C. Gilbert
- Department
of Biological Sciences, Louisiana State
University, Baton
Rouge, Louisiana 70803, United States
| | - Adam R. Offenbacher
- Department
of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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2
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Subong BJJ, Ozawa T. Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability. Curr Issues Mol Biol 2024; 46:2598-2619. [PMID: 38534781 DOI: 10.3390/cimb46030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
The nonstructural proteins 7 and 8 (nsp7 and nsp8) of SARS-CoV-2 are highly important proteins involved in the RNA-dependent polymerase (RdRp) protein replication complex. In this study, we analyzed the global mutation of nsp7 and nsp8 in 2022 and 2023 and analyzed the effects of mutation on the viral replication protein complex using bio-chemoinformatics. Frequently occurring variants are found to be single amino acid mutations for both nsp7 and nsp8. The most frequently occurring mutations for nsp7 which include L56F, L71F, S25L, M3I, D77N, V33I and T83I are predicted to cause destabilizing effects, whereas those in nsp8 are predicted to cause stabilizing effects, with the threonine to isoleucine mutation (T89I, T145I, T123I, T148I, T187I) being a frequent mutation. A conserved domain database analysis generated critical interaction residues for nsp7 (Lys-7, His-36 and Asn-37) and nsp8 (Lys-58, Pro-183 and Arg-190), which, according to thermodynamic calculations, are prone to destabilization. Trp-29, Phe-49 of nsp7 and Trp-154, Tyr-135 and Phe-15 of nsp8 cause greater destabilizing effects to the protein complex based on a computational alanine scan suggesting them as possible new target sites. This study provides an intensive analysis of the mutations of nsp7 and nsp8 and their possible implications for viral complex stability.
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Affiliation(s)
- Bryan John J Subong
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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3
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Martin MF, Bonaventure B, McCray NE, Peersen OB, Rozen-Gagnon K, Stapleford KA. Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575630. [PMID: 38293111 PMCID: PMC10827052 DOI: 10.1101/2024.01.15.575630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Alphaviruses encode an error-prone RNA-dependent RNA polymerase (RdRp), nsP4, required for genome synthesis, yet how the RdRp functions in the complete alphavirus life cycle is not well-defined. Previous work using chikungunya virus (CHIKV) has established the importance of the nsP4 residue cysteine 483 in maintaining viral genetic fidelity. Given the location of residue C483 in the nsP4 palm domain, we hypothesized that other residues within this domain and surrounding subdomains would also contribute to polymerase function. To test this hypothesis, we designed a panel of nsP4 variants via homology modeling based on the Coxsackievirus B3 3 polymerase. We rescued each variant in both mammalian and mosquito cells and discovered that the palm domain and ring finger subdomain contribute to polymerase host-specific replication and genetic stability. Surprisingly, in mosquito cells, these variants in the ring finger and palm domain were replication competent and produced viral structural proteins, but they were unable to produce infectious progeny, indicating a yet uncharacterized role for the polymerase in viral assembly. Finally, we have identified additional residues in the nsP4 palm domain that influence the genetic diversity of the viral progeny, potentially via an alteration in NTP binding and/or discrimination by the polymerase. Taken together, these studies highlight that distinct nsP4 subdomains regulate multiple processes of the alphavirus life cycle, placing nsP4 in a central role during the switch from RNA synthesis to packaging and assembly.
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Affiliation(s)
- Marie-France Martin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nia E. McCray
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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4
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Yap PG, Gan CY. Tyrosinase inhibitory peptides: Structure-activity relationship study on peptide chemical properties, terminal preferences and intracellular regulation of melanogenesis signaling pathways. Biochim Biophys Acta Gen Subj 2024; 1868:130503. [PMID: 37923180 DOI: 10.1016/j.bbagen.2023.130503] [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: 04/05/2023] [Revised: 10/08/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Bioactive peptides have gained attention as potential alternatives to chemical-based skin lightening agents. Based on literature search, the reported articles focused mainly on the sources and preparation methods of tyrosinase inhibitory peptides and there is lacking information regarding the structure-activity relationship (SAR) between peptide property and tyrosinase inhibition. It was hypothesized that peptide properties such as hydrophobicity/hydrophilicity and the amino acid type and position/arrangement at the terminal positions could affect peptide mode of binding hence result in various degrees of tyrosinase inhibition. METHODS In this study, the sequences of 128 tyrosinase inhibitory peptides were collected from peer-reviewed articles. The hydrophobicity/hydrophilicity property and the amino acid profile of peptides at the N- and C-terminals were analyzed using bioinformatics tools. Molecular docking analysis was employed to further elucidate the roles of reactive amino acids in tyrosinase-peptide binding interactions. The peptide-regulated intracellular melanogenesis pathways were also compiled and discussed. RESULTS It was found that hydrophobic and/or polar neutral properties may facilitate or stabilize peptide binding with tyrosinase. Moreover, short peptides featuring a cysteine and tyrosine at the N- and C- terminal ultimate positions tend to bind to the active site of tyrosinase whereas positively charged amino acid such as arginine at the N-terminal does not favor peptide binding to tyrosinase. CONCLUSIONS These findings provide detailed explanation on how peptide/amino acid structures are related and what function they play in tyrosinase inhibition. It could also inspire researchers to account for tyrosinase-peptide SAR and the underlying anti-melanogenesis mechanisms in formulating peptide-based treatments or strategies against skin hyperpigmentation.
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Affiliation(s)
- Pei-Gee Yap
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, University Innovation Incubator Building, SAINS@USM, Lebuh Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, University Innovation Incubator Building, SAINS@USM, Lebuh Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
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5
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Wan C, Yu S, Dang P, Gao L, Ge J, Li Y, Yang H, Yang P, Feng B, Gao J. Nitrogen regulates the synthesis of hydrophobic amino acids to improve protein structural and gel properties in common buckwheat. Int J Biol Macromol 2023; 253:126871. [PMID: 37716662 DOI: 10.1016/j.ijbiomac.2023.126871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
Nitrogen (N) fertilizer impacts the grain quality of common buckwheat, but the effects and regulatory mechanisms of N on various protein parameters of buckwheat are not fully understood. The purpose of this study was to investigate the particle morphology, structural and gel properties, and regulation mechanism of buckwheat protein under four N levels. The bulk density, surface hydrophobicity, particle size, and thermal properties of the buckwheat protein were maximized through the optimal N application (180 kg N/ha), further enhancing the thermal stability of the protein. N application increased the β-sheet content and reduced the random coil content. Appropriate N fertilizer input enhanced the tertiary structure stability and gel elasticity of buckwheat protein by promoting hydrophobic interactions, disulfide bonds, ionic bonds, storage modulus and loss modulus. The differentially expressed proteins induced by N are primarily enriched in small ribosomal subunit and ribosome, improving protein quality mainly by promoting the synthesis of hydrophobic amino acids. Future agriculture should pay attention to the hydrophobic amino acid content of buckwheat to effectively improve protein quality. This study further advances the application of buckwheat protein in the field of food processing and provides a theoretical basis for the extensive development and utilization of buckwheat protein.
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Affiliation(s)
- Chenxi Wan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China.
| | - Shaopeng Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Pengfei Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Licheng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China; Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Gent, Belgium
| | - Jiahao Ge
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Yaxin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Hao Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Pu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China
| | - Jinfeng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi Province 712100, China.
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6
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Langendörfer LJ, Avdylaj B, Hensel O, Diakité M. Design of Plant-Based Food: Influences of Macronutrients and Amino Acid Composition on the Techno-Functional Properties of Legume Proteins. Foods 2023; 12:3787. [PMID: 37893680 PMCID: PMC10606351 DOI: 10.3390/foods12203787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Imitating animal-based products using vegetable proteins is a technological challenge that can be mastered based on their techno-functional properties. These properties of legume proteins can be influenced by multiple factors, among which the macronutrients and amino acid contents play an important role. Therefore, the question arises as to what extent the techno-functional properties are related to these factors. The water- and oil-holding capacities and the emulsion and foaming properties of commercially available legume protein powders were analyzed. Correlations between macronutrient, amino acid content, steric structure, and techno-functional properties were conducted. However, the protein concentration is the focus of techno-functional properties, as well as the type of protein and the interaction with the non-protein ingredients. The type of protein is not always quantified by the quantity of amino acids or by their spatial arrangement. In this study, the effects of the three-dimensional structure were observed by the used purification method, which overshadow the influencing factors of the macronutrients and amino acid content. In summary, both the macronutrient and amino acid contents of legume proteins provide a rough indication but not a comprehensive statement about their techno-functional properties and classification in an adequate product context.
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Affiliation(s)
- Lena Johanna Langendörfer
- Faculty of Food Technology, University of Applied Science Fulda, Leipziger Str. 123, 36037 Fulda, Germany; (B.A.); (M.D.)
| | - Blerarta Avdylaj
- Faculty of Food Technology, University of Applied Science Fulda, Leipziger Str. 123, 36037 Fulda, Germany; (B.A.); (M.D.)
| | - Oliver Hensel
- Faculty of Organic Agricultural Science, University of Kassel, Nordbahnhofstraße 1a, 37213 Witzenhausen, Germany;
| | - Mamadou Diakité
- Faculty of Food Technology, University of Applied Science Fulda, Leipziger Str. 123, 36037 Fulda, Germany; (B.A.); (M.D.)
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7
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Marafie SK, Alshawaf E, Abu-Farha M, Thanaraj TA, Wei DQ, Al-Mulla F, Khan A, Abubaker J, Mohammad A. Exploring the Binding Mechanism of NRG1-ERBB3 Complex and Discovery of Potent Natural Products to Reduce Diabetes-Assisted Breast Cancer Progression. Interdiscip Sci 2023:10.1007/s12539-023-00566-y. [PMID: 37389721 PMCID: PMC10374477 DOI: 10.1007/s12539-023-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 07/01/2023]
Abstract
Diabetes mellitus significantly contributes to breast cancer progression, where hyperglycemia upregulates specific genes, leading to more aggressive tumor growth. In patients with BC that develop diabetes, neuregulin 1 (NRG1) and epidermal growth factor receptor 3 (ERBB3) overexpression exacerbate tumor growth and progression. Since the interaction between NRG1 and ERBB3 is critical for tumor growth, understanding the molecular mechanisms underlying NRG1-ERBB3 complex formation is essential for elucidating diabetes-assisted breast cancer progression. However, the key residues forming the NRG1-ERBB3 complex remain unknown. Here, we substituted specific residues in NRG1 with alanine and studied its interactions with ERBB3 using computational structural biology tools. We further screened the South African natural compounds database to target the complex's interface residues to discover potential inhibitors. The conformational stability and dynamic features of NRG1-WT, -H2A, -L3A, and -K35A complexed with ERBB3 were subjected to 400 ns molecular dynamics simulations. The free binding energies of all NRG1-ERBB3 complexes were calculated using the molecular mechanics-generalized Born surface area (MM/GBSA). The H2 and L3 alanine substitutions caused a loss of interaction with ERBB3 residue D73, weakening the interaction with ERBB3. Screening 1300 natural compounds identified four (SANC00643, SANC00824, SANC00975, and SANC00335) with the best potential to inhibit ERRB3-NRG1 coupling. The binding free energies for each complex were - 48.55 kcal/mol for SANC00643, - 47.68 kcal/mol for SANC00824, - 46.04 kcal/mol for SANC00975, and - 45.29 kcal/mol for SANC00335, showing their overall stronger binding with ERBB3 than NRG1 and their potential to act as ERBB3-NRG1 complex inhibitors. In conclusion, this complex may represent a residue-specific drug target to inhibit BC progression.
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Affiliation(s)
- Sulaiman K Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
- Special Service Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | | | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait.
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait.
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8
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Zaragoza JPT, Offenbacher AR, Hu S, Gee CL, Firestein ZM, Minnetian N, Deng Z, Fan F, Iavarone AT, Klinman JP. Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Proc Natl Acad Sci U S A 2023; 120:e2211630120. [PMID: 36867685 PMCID: PMC10013837 DOI: 10.1073/pnas.2211630120] [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: 07/06/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation (Ea) for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Adam R. Offenbacher
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, East Carolina University, Greenville, NC27858
| | - Shenshen Hu
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
| | | | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Flora Fan
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
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9
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Ozcan A, Keskin O, Sariyar Akbulut B, Ozbek P. Piperidine-based natural products targeting Type IV pili antivirulence: A computational approach. J Mol Graph Model 2023; 119:108382. [PMID: 36463631 DOI: 10.1016/j.jmgm.2022.108382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/01/2022] [Accepted: 11/23/2022] [Indexed: 11/28/2022]
Abstract
Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dynamic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.
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Affiliation(s)
- Aslihan Ozcan
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Ozlem Keskin
- College of Engineering, Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Berna Sariyar Akbulut
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey.
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10
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Gheorghita AA, Li YE, Kitova EN, Bui DT, Pfoh R, Low KE, Whitfield GB, Walvoort MTC, Zhang Q, Codée JDC, Klassen JS, Howell PL. Structure of the AlgKX modification and secretion complex required for alginate production and biofilm attachment in Pseudomonas aeruginosa. Nat Commun 2022; 13:7631. [PMID: 36494359 PMCID: PMC9734138 DOI: 10.1038/s41467-022-35131-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Synthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are organized to coordinate polymer biosynthesis, modification, and export across both membranes and the peptidoglycan. To investigate how synthase-dependent secretion systems produce polymer at a molecular level, we determined the crystal structure of the AlgK-AlgX (AlgKX) complex involved in Pseudomonas aeruginosa alginate exopolysaccharide acetylation and export. We demonstrate that AlgKX directly binds alginate oligosaccharides and that formation of the complex is vital for polymer production and biofilm attachment. Finally, we propose a structural model for the AlgEKX outer membrane modification and secretion complex. Together, our study provides insight into how alginate biosynthesis proteins coordinate production of a key exopolysaccharide involved in establishing persistent Pseudomonas lung infections.
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Affiliation(s)
- Andreea A. Gheorghita
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
| | - Yancheng E. Li
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.20861.3d0000000107068890Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Duong T. Bui
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Roland Pfoh
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Kristin E. Low
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.55614.330000 0001 1302 4958Present Address: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Gregory B. Whitfield
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC Canada
| | - Marthe T. C. Walvoort
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.4830.f0000 0004 0407 1981Present Address: Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Qingju Zhang
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.411862.80000 0000 8732 9757Present Address: National Research Centre for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, China
| | - Jeroen D. C. Codée
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - P. Lynne Howell
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
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11
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Chu AE, Fernandez D, Liu J, Eguchi RR, Huang PS. De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design. BIODESIGN RESEARCH 2022; 2022:9842315. [PMID: 37850141 PMCID: PMC10521652 DOI: 10.34133/2022/9842315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 10/19/2023] Open
Abstract
The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.
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Affiliation(s)
- Alexander E Chu
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, And Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
| | - Jingjia Liu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
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12
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Shi M, Qi L, He LS. Comparative Analysis of the Mitochondrial Genome of Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae) From a Depth of 9,462 m at the Mariana Trench. Front Genet 2022; 13:854009. [PMID: 35754826 PMCID: PMC9213748 DOI: 10.3389/fgene.2022.854009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
The hadal zone, which represents the deepest marine habitat on Earth (6,000–11,000 m), is a harsh environment mainly characterized by extremely high hydrostatic pressure, and this habitat is believed to have a high degree of endemism. The deep-sea anemone family Galatheanthemidae comprises two valid species exclusively from the hadal; however, no other information about this family is currently available. In the present study, a sea anemone was collected from a depth of 9,462 m at the Mariana Trench and was defined as Galatheanthemum sp. MT-2020 (Actiniaria Galatheanthemidae). The mitochondrial genome of Galatheanthemum sp. MT-2020 was circular, was 16,633 bp in length, and contained two ribosomal RNA genes, 13 protein-coding genes and two transfer RNA genes. The order of the genes of Galatheanthemum sp. MT-2020 was identical to that of the majority of the species of the order Actiniaria. The value of the AT-skew was the lowest in the whole mitochondrial genome, with a positive GC skew value for the atp8 gene, while other species, except Antholoba achates, had the negative values of the GC skew. Galatheanthemum sp. MT-2020 was clustered with another abyssal species, Paraphelliactis xishaensis, in the phylogenetic tree, and these species diverged in the early Jurassic approximately 200 Mya from the shallow-sea species. The usage ratio of valine, which is one of the five amino acids with the strongest barophilic properties, in the mitochondrial genomes of the two abyssal species was significantly higher than that in other species with habitats above the depth of 3,000 m. The ω (dN/dS) ratio of the genomes was 2.45-fold higher than that of the shallow-sea species, indicating a slower evolutionary rate. Overall, the present study is the first to provide a complete mitogenome of sea anemones from the hadal and reveal some characteristics that may be associated with adaptation to an extreme environment.
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Affiliation(s)
- Mengke Shi
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Qi
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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13
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Pant K, Thakur M, Chopra HK, Dar BN, Nanda V. Assessment of fatty acids, amino acids, minerals, and thermal properties of bee propolis from Northern India using a multivariate approach. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
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Affiliation(s)
- Dustin C. Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T. Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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15
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Zhen N, Ye C, Shen Q, Zeng X, Wu Z, Guo Y, Cai Z, Pan D. Heterologous expression and biological characteristics of UGPases from Lactobacillus acidophilus. Appl Microbiol Biotechnol 2022; 106:2481-2491. [PMID: 35344091 DOI: 10.1007/s00253-022-11856-8] [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: 08/05/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 11/24/2022]
Abstract
Herein, two genes (LBA0625 and LBA1719) encoding UGPases (UDP-glucose pyrophosphorylase) in Lactobacillus acidophilus (L. acidophilus) were successfully transformed into Escherichia coli BL21 (DE3) to construct recombinant overexpressing strains (E-0625, E-1719) to investigate the biological characteristics of UGPase-0625 and UGPase-1719. The active sites, polysaccharide yield, and anti-freeze-drying stress of L. acidophilus ATCC4356 were also detected. UGPase-0625 and UGPase-1719 belong to the nucleotidyltransferase of stable hydrophilic proteins; contain 300 and 294 amino acids, respectively; and have 20 conserved active sites by prediction. Αlpha-helixes and random coils were the main secondary structures, which constituted the main skeleton of UGPases. The optimal mixture for the high catalytic activity of the two UGPases included 0.5 mM UDP-Glu (uridine diphosphate glucose) and Mg2+ at 37 °C, pH 10.0. By comparing the UGPase activities of the mutant strains with the original recombinant strains, A10, L130, and L263 were determined as the active sites of UGPase-0625 (P < 0.01) and A11, L130, and L263 were determined as the active sites of UGPase-1719 (P < 0.01). In addition, UGPase overexpression could increase the production of polysaccharides and the survival rates of recombinant bacteria after freeze-drying. This is the first study to determine the enzymatic properties, active sites, and structural simulation of UGPases from L. acidophilus, providing in-depth understanding of the biological characteristics of UGPases in lactic acid bacteria.Key points• We detected the biological characteristics of UGPases encoded by LBA0625 and LBA1719.• We identified UGPase-0625 and UGPase-1719 active sites.• UGPase overexpression elevates polysaccharide levels and post-freeze-drying survival.
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Affiliation(s)
- Ni Zhen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Congyan Ye
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Qiyuan Shen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Xiaoqun Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China. .,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China.
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Yuxing Guo
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210097, China
| | - Zhendong Cai
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo, 315211, China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315800, China.,College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
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16
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Fernández-Lucas J, Acebrón I, Wu RY, Alfaro Y, Acosta J, Kaminski PA, Arroyo M, Joachimiak A, Nocek BP, De la Mata I, Mancheño JM. Biochemical and structural studies of two tetrameric nucleoside 2'-deoxyribosyltransferases from psychrophilic and mesophilic bacteria: Insights into cold-adaptation. Int J Biol Macromol 2021; 192:138-150. [PMID: 34624379 DOI: 10.1016/j.ijbiomac.2021.09.164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Nucleoside 2'-deoxyribosyltransferases (NDTs) catalyze the cleavage of glycosidic bonds of 2'-deoxynucleosides and the following transfer of the 2'-deoxyribose moiety to acceptor nucleobases. Here, we report the crystal structures and biochemical properties of the first tetrameric NDTs: the type I NDT from the mesophilic bacterium Enterococcus faecalis V583 (EfPDT) and the type II NDT from the bacterium Desulfotalea psychrophila (DpNDT), the first psychrophilic NDT. This novel structural and biochemical data permitted an exhaustive comparative analysis aimed to shed light into the basis of the high global stability of the psychrophilic DpNDT, which has a higher melting temperature than EfPDT (58.5 °C versus 54.4 °C) or other mesophilic NDTs. DpNDT possesses a combination of unusual structural motifs not present neither in EfPDT nor any other NDT that most probably contribute to its global stability, in particular, a large aliphatic isoleucine-leucine-valine (ILV) bundle accompanied by a vicinal disulfide bridge and also an intersubunit disulfide bridge, the first described for an NDT. The functional and structural features of DpNDT do not fit the standard features of psychrophilic enzymes, which lead us to consider the implication of (sub)cellular levels together with the protein level in the adaptation of enzymatic activity to low temperatures.
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Affiliation(s)
- Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 66, Barranquilla, Colombia
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Ruiying Y Wu
- Bioscience Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yohana Alfaro
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Pierre A Kaminski
- Institut Pasteur, Unite ́Biologie des Bactéries Pathogènes à Gram-positif, CNRS URL3526, Paris, France
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - Andrzej Joachimiak
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60367, USA
| | - Boguslaw P Nocek
- Bioscience Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Isabel De la Mata
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain.
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17
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Leavens MJ, Spang LE, Cherney MM, Bowler BE. Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues. Biochemistry 2021; 60:3071-3085. [PMID: 34606713 PMCID: PMC8751257 DOI: 10.1021/acs.biochem.1c00400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris cytochrome c', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome c (iso-1-Cytc). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cytc domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.
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Affiliation(s)
- Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Lisa E. Spang
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Melisa M. Cherney
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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18
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Transcriptomics and Metabolomics Analyses Provide Novel Insights into Glucose-Induced Trophic Transition of the Marine Diatom Nitzschia laevis. Mar Drugs 2021; 19:md19080426. [PMID: 34436265 PMCID: PMC8401676 DOI: 10.3390/md19080426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
Diatoms have important ecological roles and are natural sources of bioactive compounds. Nitzschia laevis is a member of marine diatoms that accumulates high-value products including fucoxanthin and eicosapentaenoic acid (EPA). In this study, physiological data showed that comparing to autotrophic growth, mixotrophic cultivation with glucose supplementation led to a decrease of chlorophyll and fucoxanthin content in N. laevis, and an increase of biomass density and EPA yield. To further examine the metabolic barriers for fucoxanthin and EPA biosynthesis, comparative transcriptomic and metabolome analyses were conducted, with a focus on the genes related to carotenoids biosynthesis and fatty acid metabolism. The results indicated that phytoene desaturase (PDS) and zeta-carotene isomerase (ZISO) could be the rate-limiting enzymes in carotenoid biosynthesis. The transcription regulation of 3-ketoacyl-CoA synthase (KCS) and elongation of very long chain fatty acids protein (EVOVL) are important contributors associated with polyunsaturated fatty acids (PUFAs) accumulation. Furthermore, we also investigated the glucose-associated regulatory genes using weighted gene co-expression network analysis, and identified potential hub genes linked with cell cycle, carbohydrate metabolism, purine biosynthesis, and lipid metabolism. This study offers a high-quality transcriptome resource for N. laevis and provides a molecular framework for further metabolic engineering studies on fucoxanthin and EPA production.
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Ferruz N, Schmidt S, Höcker B. ProteinTools: a toolkit to analyze protein structures. Nucleic Acids Res 2021; 49:W559-W566. [PMID: 34019657 PMCID: PMC8262690 DOI: 10.1093/nar/gkab375] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/11/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023] Open
Abstract
The experimental characterization and computational prediction of protein structures has become increasingly rapid and precise. However, the analysis of protein structures often requires researchers to use several software packages or web servers, which complicates matters. To provide long-established structural analyses in a modern, easy-to-use interface, we implemented ProteinTools, a web server toolkit for protein structure analysis. ProteinTools gathers four applications so far, namely the identification of hydrophobic clusters, hydrogen bond networks, salt bridges, and contact maps. In all cases, the input data is a PDB identifier or an uploaded structure, whereas the output is an interactive dynamic web interface. Thanks to the modular nature of ProteinTools, the addition of new applications will become an easy task. Given the current need to have these tools in a single, fast, and interpretable interface, we believe that ProteinTools will become an essential toolkit for the wider protein research community. The web server is available at https://proteintools.uni-bayreuth.de.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Steffen Schmidt
- Computational Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
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20
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A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family. Proc Natl Acad Sci U S A 2021; 118:2019571118. [PMID: 33875592 PMCID: PMC8092565 DOI: 10.1073/pnas.2019571118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Orthologous proteins from the three superkingdoms have conserved their structures and functions over evolutionary time. We ask whether their folding mechanisms and the structures of their partially folded states are similarly conserved, using bacterial and archaeal representatives of the IGPS TIM barrel enzyme. Comparison of circular dichroism and fluorescence spectroscopic studies reveal a highly conserved mechanism, and hydrogen–deuterium exchange mass spectrometry analyses highlight similar cores of stability in regions dominated by clusters of branched aliphatic side chains. A bioinformatics analysis of hundreds of IGPS sequences from each superkingdom shows a very highly conserved sequence, V/ILLI, that nucleates the formation of a misfolded, microsecond intermediate and has existed since the last universal common ancestor of the IGPS family of proteins. The amino acid sequences of proteins have evolved over billions of years, preserving their structures and functions while responding to evolutionary forces. Are there conserved sequence and structural elements that preserve the protein folding mechanisms? The functionally diverse and ancient (βα)1–8 TIM barrel motif may answer this question. We mapped the complex six-state folding free energy surface of a ∼3.6 billion y old, bacterial indole-3-glycerol phosphate synthase (IGPS) TIM barrel enzyme by equilibrium and kinetic hydrogen–deuterium exchange mass spectrometry (HDX-MS). HDX-MS on the intact protein reported exchange in the native basin and the presence of two thermodynamically distinct on- and off-pathway intermediates in slow but dynamic equilibrium with each other. Proteolysis revealed protection in a small (α1β2) and a large cluster (β5α5β6α6β7) and that these clusters form cores of stability in Ia and Ibp. The strongest protection in both states resides in β4α4 with the highest density of branched aliphatic side chain contacts in the folded structure. Similar correlations were observed previously for an evolutionarily distinct archaeal IGPS, emphasizing a key role for hydrophobicity in stabilizing common high-energy folding intermediates. A bioinformatics analysis of IGPS sequences from the three superkingdoms revealed an exceedingly high hydrophobicity and surprising α-helix propensity for β4, preceded by a highly conserved βα-hairpin clamp that links β3 and β4. The conservation of the folding mechanisms for archaeal and bacterial IGPS proteins reflects the conservation of key elements of sequence and structure that first appeared in the last universal common ancestor of these ancient proteins.
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21
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Lau CYJ, Fontana F, Mandemaker LDB, Wezendonk D, Vermeer B, Bonvin AMJJ, de Vries R, Zhang H, Remaut K, van den Dikkenberg J, Medeiros-Silva J, Hassan A, Perrone B, Kuemmerle R, Gelain F, Hennink WE, Weingarth M, Mastrobattista E. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Commun Chem 2020; 3:164. [PMID: 36703336 PMCID: PMC9814929 DOI: 10.1038/s42004-020-00417-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023] Open
Abstract
Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.
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Affiliation(s)
- Chun Yin Jerry Lau
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Federico Fontana
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy
| | - Laurens D. B. Mandemaker
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Dennie Wezendonk
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Benjamin Vermeer
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- grid.4818.50000 0001 0791 5666Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Heyang Zhang
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Katrien Remaut
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Joep van den Dikkenberg
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - João Medeiros-Silva
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alia Hassan
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Barbara Perrone
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Fabrizio Gelain
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy ,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell’Ospedale Maggiore 3, 20162 Milan, Italy
| | - Wim E. Hennink
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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22
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Mojsak P, Rey-Stolle F, Parfieniuk E, Kretowski A, Ciborowski M. The role of gut microbiota (GM) and GM-related metabolites in diabetes and obesity. A review of analytical methods used to measure GM-related metabolites in fecal samples with a focus on metabolites' derivatization step. J Pharm Biomed Anal 2020; 191:113617. [PMID: 32971497 DOI: 10.1016/j.jpba.2020.113617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
Disruption of gut microbiota (GM) composition is increasingly related to the pathogenesis of various metabolic diseases. Additionally, GM is responsible for the production and transformation of metabolites involved in the development of metabolic disorders, such as obesity and type 2 diabetes mellitus (T2DM). The current state of knowledge regarding the composition of GM and GM-related metabolites in relation to the progress and development of obesity and T2DM is presented in this review. To understand the relationships between GM-related metabolites and the development of metabolic disorders, their accurate qualitative and quantitative measurement in biological samples is needed. Feces represent a valuable biological matrix which composition may reflect the health status of the lower gastrointestinal tract and the whole organism. Mass spectrometry (MS), mainly in combination with gas chromatography (GC) or liquid chromatography (LC), is commonly used to measure fecal metabolites. However, profiling metabolites in such a complex matrix as feces is challenging from both analytical chemistry and biochemistry standpoints. Chemical derivatization is one of the most effective methods used to overcome these problems. In this review, we provide a comprehensive summary of the derivatization methods of GM-related metabolites prior to GC-MS or LC-MS analysis, which have been published in the last five years (2015-2020). Additionally, analytical methods used for the analysis of GM-related metabolites without the derivatization step are also presented.
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Affiliation(s)
- Patrycja Mojsak
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ewa Parfieniuk
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland.
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23
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Liu W, Barbosa Dos Santos I, Moye A, Park SW. CYP20-3 deglutathionylates 2-CysPRX A and suppresses peroxide detoxification during heat stress. Life Sci Alliance 2020; 3:e202000775. [PMID: 32732254 PMCID: PMC7409537 DOI: 10.26508/lsa.202000775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/24/2022] Open
Abstract
In plants, growth-defense trade-offs occur because of limited resources, which demand prioritization towards either of them depending on various external and internal factors. However, very little is known about molecular mechanisms underlying their occurrence. Here, we describe that cyclophilin 20-3 (CYP20-3), a 12-oxo-phytodienoic acid (OPDA)-binding protein, crisscrosses stress responses with light-dependent electron reactions, which fine-tunes activities of key enzymes in plastid sulfur assimilations and photosynthesis. Under stressed states, OPDA, accumulates in the chloroplasts, binds and stimulates CYP20-3 to convey electrons towards serine acetyltransferase 1 (SAT1) and 2-Cys peroxiredoxin A (2CPA). The latter is a thiol-based peroxidase, protecting and optimizing photosynthesis by reducing its toxic byproducts (e.g., H2O2). Reduction of 2CPA then inactivates its peroxidase activity, suppressing the peroxide detoxification machinery, whereas the activation of SAT1 promotes thiol synthesis and builds up reduction capacity, which in turn triggers the retrograde regulation of defense gene expressions against abiotic stress. Thus, we conclude that CYP20-3 is a unique metabolic hub conveying resource allocations between plant growth and defense responses (trade-offs), ultimately balancing optimal growth phonotype.
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Affiliation(s)
- Wenshan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | - Anna Moye
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Sang-Wook Park
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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24
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Abstract
The role of alpha-synuclein (αS) amyloid fibrillation has been recognized in various neurological diseases including Parkinson's Disease (PD). In early stages, fibrillation occurs by the structural transition from helix to extended states in monomeric αS followed by the formation of beta-sheets. This alpha-helix to beta-sheet transition (αβT) speeds up the formation of amyloid fibrils through the formation of unstable and temporary configurations of the αS. In this study, the most important regions that act as initiating nuclei and make unstable the initial configuration were identified based on sequence and structural information. In this regard, a Targeted Molecular Dynamics (TMD) simulation was employed using explicit solvent models under physiological conditions. Identified regions are those that are in the early steps of structural opening. The trajectory was clustered the structures characterized the intermediate states. The findings of this study would help us to better understanding of the mechanism of amyloid fibril formation.
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25
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Anggayasti WL, Ogino K, Yamamoto E, Helmerhorst E, Yasuoka K, Mancera RL. The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study. Comput Struct Biotechnol J 2020; 18:1160-1172. [PMID: 32514327 PMCID: PMC7261955 DOI: 10.1016/j.csbj.2020.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/02/2022] Open
Abstract
High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer's disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptors (TLRs). The acidic C-terminal tail of HMGB1 is an intrinsically disordered region of the protein which is known to determine the interaction of HMGB1 to DNA and histones. This study characterizes its structural properties using a combination of circular dichroism (CD) and molecular dynamics (MD) simulations. The full-length and tail-less forms of HMGB1 were compared to rationalise the role of the acidic tail in maintaining the stability of the entire structure of HMGB1 in atomistic detail. Consistent with experimental data, the acidic tail was predicted to adopt an extended conformation that allows it to make a range of hydrogen-bonding and electrostatic interactions with the box-like domains that stabilize the overall structure of HMGB1. Absence of the acidic tail was predicted to increase structural fluctuations of all amino acids, leading to changes in secondary structure from α-helical to more hydrophilic turns along with increased exposure of multiple amino acids to the surrounding solvent. These structural changes reveal the intrinsic conformational dynamics of HMGB1 that are likely to affect the accessibility of its receptors.
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Affiliation(s)
- Wresti L. Anggayasti
- Department of Chemical Engineering, Faculty of Engineering, Brawijaya University, Jl. MT Haryono 167, Malang 65145, East Java, Indonesia
| | - Kenta Ogino
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Erik Helmerhorst
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ricardo L. Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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26
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Santiago Á, Razo-Hernández RS, Pastor N. Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. J Chem Inf Model 2020; 60:866-879. [PMID: 31917925 DOI: 10.1021/acs.jcim.9b00824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The TATA-box binding protein (TBP) is an important element of the transcription machinery in archaea and eukaryotic organisms. TBP is expressed in organisms adapted to different temperatures, indicating a robust structure, and experimental studies have shown that the mid-unfolding temperature (Tm) of TBP is directly correlated with the optimal growth temperature (OGT) of the organism. To understand which are the relevant structural requirements for its stability, we present the first structural and dynamic computational study of TBPs, combining molecular dynamics (MD) simulations and a quantitative structure-property relationship (QSPR) over a set of TBPs of organisms adapted to different temperatures. We found that the main structural properties of TBP used to adapt to high temperatures are an increase in the ease of desolvation of charged residues at the surface, an increase in the local resiliency, the presence of Leu clusters in the protein core, and an increase in the loss of hydrophobic packing in the N-terminal subdomain. In view of our results, we consider that TBP is a good model to study thermal adaptation, and our analysis opens the possibility of performing protein engineering on TBPs to study transcription at high or low temperatures.
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Affiliation(s)
- Ángel Santiago
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Nina Pastor
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología , Universidad Nacional Autónoma de México , Av. Universidad 2001, Col. Chamilpa , Cuernavaca , Morelos 62210 , México
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27
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Pollack JD, Gerard D, Makhatadze GI, Pearl DK. Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence. J Biomol Struct Dyn 2019; 38:3700-3719. [DOI: 10.1080/07391102.2019.1679666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- J. Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, USA
| | - George I. Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Dennis K. Pearl
- Department of Statistics, Penn State University, University Park, Pennsylvania, USA
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28
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Abstract
Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecular-level understanding of the readout from sequence to structure. We have combined sequence-sensitive native centric simulations with small-angle X-ray scattering and time-resolved Förster resonance energy transfer to monitor the formation of structure in an intermediate in the Sulfolobus solfataricus indole-3-glycerol phosphate synthase TIM barrel that appears within 50 μs and must at least partially unfold to achieve productive folding. Simulations reveal the presence of a major and 2 minor folding channels not detected in experiments. Frustration in folding, i.e., backtracking in native contacts, is observed in the major channel at the initial stage of folding, as well as late in folding in a minor channel before the appearance of the native conformation. Similarities in global and pairwise dimensions of the early intermediate, the formation of structure in the central region that spreads progressively toward each terminus, and a similar rate-limiting step in the closing of the β-barrel underscore the value of combining simulation and experiment to unravel complex folding mechanisms at the molecular level.
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29
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Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions. Proc Natl Acad Sci U S A 2019; 116:12301-12310. [PMID: 31167941 PMCID: PMC7056937 DOI: 10.1073/pnas.1818206116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteins are marginally stable molecules that fluctuate between folded and unfolded states. Here, we provide a high-resolution description of unfolded states under refolding conditions for the N-terminal domain of the L9 protein (NTL9). We use a combination of time-resolved Förster resonance energy transfer (FRET) based on multiple pairs of minimally perturbing labels, time-resolved small-angle X-ray scattering (SAXS), all-atom simulations, and polymer theory. Upon dilution from high denaturant, the unfolded state undergoes rapid contraction. Although this contraction occurs before the folding transition, the unfolded state remains considerably more expanded than the folded state and accommodates a range of local and nonlocal contacts, including secondary structures and native and nonnative interactions. Paradoxically, despite discernible sequence-specific conformational preferences, the ensemble-averaged properties of unfolded states are consistent with those of canonical random coils, namely polymers in indifferent (theta) solvents. These findings are concordant with theoretical predictions based on coarse-grained models and inferences drawn from single-molecule experiments regarding the sequence-specific scaling behavior of unfolded proteins under folding conditions.
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30
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Tavella D, Zitzewitz JA, Massi F. Characterization of TDP-43 RRM2 Partially Folded States and Their Significance to ALS Pathogenesis. Biophys J 2018; 115:1673-1680. [PMID: 30309612 PMCID: PMC6224623 DOI: 10.1016/j.bpj.2018.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/07/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The human protein TDP-43 is a major component of the cellular aggregates found in amyotrophic lateral sclerosis and other neurodegenerative diseases. Insoluble cytoplasmic aggregates isolated from the brain of amyotrophic lateral sclerosis and frontotemporal lobar degeneration patients contain ubiquitinated, hyperphosphorylated, and N-terminally truncated TDP-43. Truncated fragments of TDP-43 identified from patient tissues contain part of the second RNA recognition motif (RRM2) and the disordered C-terminus, indicating that both domains can be involved in aggregation and toxicity. Here, we focus on RRM2. Using all-atom replica-averaged metadynamics simulations with NMR chemical shift restraints, we characterized the atomic structure of non-native states of RRM2, sparsely populated under native conditions. These structures reveal the exposure to the solvent of aggregation-prone peptide regions, normally buried in the native state, supporting a role in aggregation for the partially folded states of RRM2.
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Affiliation(s)
- Davide Tavella
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
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31
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Gonzalez-Martinez D, Johnston JR, Landim-Vieira M, Ma W, Antipova O, Awan O, Irving TC, Bryant Chase P, Pinto JR. Structural and functional impact of troponin C-mediated Ca 2+ sensitization on myofilament lattice spacing and cross-bridge mechanics in mouse cardiac muscle. J Mol Cell Cardiol 2018; 123:26-37. [PMID: 30138628 DOI: 10.1016/j.yjmcc.2018.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/26/2018] [Accepted: 08/05/2018] [Indexed: 12/25/2022]
Abstract
Acto-myosin cross-bridge kinetics are important for beat-to-beat regulation of cardiac contractility; however, physiological and pathophysiological mechanisms for regulation of contractile kinetics are incompletely understood. Here we explored whether thin filament-mediated Ca2+ sensitization influences cross-bridge kinetics in permeabilized, osmotically compressed cardiac muscle preparations. We used a murine model of hypertrophic cardiomyopathy (HCM) harboring a cardiac troponin C (cTnC) Ca2+-sensitizing mutation, Ala8Val in the regulatory N-domain. We also treated wild-type murine muscle with bepridil, a cTnC-targeting Ca2+ sensitizer. Our findings suggest that both methods of increasing myofilament Ca2+ sensitivity increase cross-bridge cycling rate measured by the rate of tension redevelopment (kTR); force per cross-bridge was also enhanced as measured by sinusoidal stiffness and I1,1/I1,0 ratio from X-ray diffraction. Computational modeling suggests that Ca2+ sensitization through this cTnC mutation or bepridil accelerates kTR primarily by promoting faster cross-bridge detachment. To elucidate if myofilament structural rearrangements are associated with changes in kTR, we used small angle X-ray diffraction to simultaneously measure myofilament lattice spacing and isometric force during steady-state Ca2+ activations. Within in vivo lattice dimensions, lattice spacing and steady-state isometric force increased significantly at submaximal activation. We conclude that the cTnC N-domain controls force by modulating both the number and rate of cycling cross-bridges, and that the both methods of Ca2+ sensitization may act through stabilization of cTnC's D-helix. Furthermore, we propose that the transient expansion of the myofilament lattice during Ca2+ activation may be an additional factor that could increase the rate of cross-bridge cycling in cardiac muscle. These findings may have implications for the pathophysiology of HCM.
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Affiliation(s)
- David Gonzalez-Martinez
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Weikang Ma
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Olga Antipova
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA; X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Omar Awan
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Thomas C Irving
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - J Renato Pinto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA.
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32
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Stone NP, Hilbert BJ, Hidalgo D, Halloran KT, Lee J, Sontheimer EJ, Kelch BA. A Hyperthermophilic Phage Decoration Protein Suggests Common Evolutionary Origin with Herpesvirus Triplex Proteins and an Anti-CRISPR Protein. Structure 2018; 26:936-947.e3. [PMID: 29779790 PMCID: PMC6277972 DOI: 10.1016/j.str.2018.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/16/2018] [Accepted: 04/10/2018] [Indexed: 11/18/2022]
Abstract
Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs. Our analysis of the gp87 structure reveals that the core "β tulip" domain is conserved in trimeric capsid components across numerous double-stranded DNA viruses, including Herpesviruses. Moreover, this β barrel domain is found in anti-CRISPR protein AcrIIC1, suggesting a mechanism for the evolution of this Cas9 inhibitor. Our work illustrates the principles for increased stability of gp87, and extends the evolutionary reach of the β tulip domain.
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Affiliation(s)
- Nicholas P Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Daniel Hidalgo
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kevin T Halloran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jooyoung Lee
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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33
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Kumar V, Chaudhuri TK. Spontaneous refolding of the large multidomain protein malate synthase G proceeds through misfolding traps. J Biol Chem 2018; 293:13270-13283. [PMID: 29959230 DOI: 10.1074/jbc.ra118.003903] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/28/2018] [Indexed: 11/06/2022] Open
Abstract
Most protein folding studies until now focus on single domain or truncated proteins. Although great insights in the folding of such systems has been accumulated, very little is known regarding the proteins containing multiple domains. It has been shown that the high stability of domains, in conjunction with inter-domain interactions, manifests as a frustrated energy landscape, causing complexity in the global folding pathway. However, multidomain proteins despite containing independently foldable, loosely cooperative sections can fold into native states with amazing speed and accuracy. To understand the complexity in mechanism, studies were conducted previously on the multidomain protein malate synthase G (MSG), an enzyme of the glyoxylate pathway with four distinct and adjacent domains. It was shown that the protein refolds to a functionally active intermediate state at a fast rate, which slowly produces the native state. Although experiments decoded the nature of the intermediate, a full description of the folding pathway was not elucidated. In this study, we use a battery of biophysical techniques to examine the protein's folding pathway. By using multiprobe kinetics studies and comparison with the equilibrium behavior of protein against urea, we demonstrate that the unfolded polypeptide undergoes conformational compaction to a misfolded intermediate within milliseconds of refolding. The misfolded product appears to be stabilized under moderate denaturant concentrations. Further folding of the protein produces a stable intermediate, which undergoes partial unfolding-assisted large segmental rearrangements to achieve the native state. This study reveals an evolved folding pathway of the multidomain protein MSG, which involves surpassing the multiple misfolding traps during refolding.
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Affiliation(s)
- Vipul Kumar
- From the Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India
| | - Tapan K Chaudhuri
- From the Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India
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34
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Holehouse AS, Pappu RV. Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. Annu Rev Biophys 2018; 47:19-39. [PMID: 29345991 PMCID: PMC10740066 DOI: 10.1146/annurev-biophys-070317-032838] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents.
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Affiliation(s)
- Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
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35
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Yan SH, Zhao NW, Geng ZR, Shen JY, Liu FM, Yan D, Zhou J, Nie C, Huang CC, Fang ZY. Modulations of Keap1-Nrf2 signaling axis by TIIA ameliorated the oxidative stress-induced myocardial apoptosis. Free Radic Biol Med 2018; 115:191-201. [PMID: 29221988 DOI: 10.1016/j.freeradbiomed.2017.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/26/2017] [Accepted: 12/01/2017] [Indexed: 01/16/2023]
Abstract
Mounting evidence has strongly implicated oxidative stress in the development of cardiac dysfunction, and myocardial apoptosis contributes to the pathogenesis of heart failure. Quantitative cardiac proteomics data revealed that pressure load by TAC resulted in a significant decline in mitochondrial metabolic activity, where TIIA (Tanshinone IIA sulfonate) treatment reversed it in vivo, which might be mediated by Nrf2. In NRVMs, TIIA treatment ameliorated H2O2-induced caspase-3/9 activations through the suppression of p38 and mTOR signaling pathways, where caspase-mediated cleavage of YY1 and PARP resulted in the defects in mitochondrial biogenesis and DNA repair, and this event finally led to cardiomyocyte apoptosis. Mass spectrometry analysis showed that TIIA hydrophobically interacted with Keap1 (the cytoplasmic repressor of Nrf2) and induced its degradation in vitro. Site-directed mutagenesis of Keap1 identified V122/V123/I125 to be the critical residues for the TIIA-induced de-dimerization and degradation of Keap1. Besides, TIIA treatment also epigenetically up-regulated Nrf2 gene transcription, where it hypomethylated the first 5 CpGs of Nrf2 promoter. Furthermore, cardiac-specific Nrf2 knockout mice exhibited the significantly dampened anti-apoptotic effects of TIIA.
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Affiliation(s)
- Shi-Hai Yan
- Laboratory of Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China; State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China
| | - Ning-Wei Zhao
- Laboratory of Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China; Shimadzu Biomedical Research Laboratory, Shanghai, China.
| | - Zhi-Rong Geng
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China
| | - Jia-Yin Shen
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Fu-Ming Liu
- Department of Cardiovascular Diseases, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Dong Yan
- Department of Cardiovascular Diseases, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jie Zhou
- Department of Pharmacology, Jiangsu Jiankang Vocational College, Nanjing, China
| | - Chao Nie
- Department of Pharmacology, Jiangsu Jiankang Vocational College, Nanjing, China
| | | | - Zhu-Yuan Fang
- Laboratory of Pharmacology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China; Department of Cardiovascular Diseases, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
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36
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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37
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Prakash A, Kumar V, Meena NK, Hassan MI, Lynn AM. Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43). J Biomol Struct Dyn 2018; 37:178-194. [DOI: 10.1080/07391102.2017.1422026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M. Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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38
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Morgan BR, Zitzewitz JA, Massi F. Structural Rearrangement upon Fragmentation of the Stability Core of the ALS-Linked Protein TDP-43. Biophys J 2017; 113:540-549. [PMID: 28793209 DOI: 10.1016/j.bpj.2017.06.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult degenerative motor neuron disease. Experimental evidence indicates a direct role of transactive-response DNA-binding protein 43 (TDP-43) in the pathology of ALS and other neurodegenerative diseases. TDP-43 has been identified as a major component of cytoplasmic inclusions in patients with sporadic ALS; however, the molecular basis of the disease mechanism is not yet fully understood. Fragmentation within the second RNA recognition motif (RRM2) of TDP-43 has been observed in patient tissues and may play a role in the formation of aggregates in disease. To determine the structural and dynamical changes resulting from the truncation that could lead to aggregation and toxicity, we performed molecular dynamics simulations of the full-length RRM2 domain (the stability core of TDP-43) and of a truncated variant (where residues 189-207 are deleted to mimic a site of cleavage within RRM2 found in ALS patients). Our simulations show heterogeneous structural reorganization and decreased stability of the truncated RRM2 domain compared to the full-length domain, consistent with previous experimental results. The decreased stability and structural reorganization in the truncated RRM2 result in a higher probability of protein-protein interactions through altered electrostatic surface charges and increased accessibility of hydrophobic residues (including the nuclear export sequence), providing a rationale for the increased cytoplasmic aggregation of RRM2 fragments seen in sporadic ALS patients.
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Affiliation(s)
- Brittany R Morgan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts
| | - Francesca Massi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts.
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39
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English CA, Sherman W, Meng W, Gierasch LM. The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. J Biol Chem 2017; 292:14765-14774. [PMID: 28754691 DOI: 10.1074/jbc.m117.789313] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Indexed: 12/20/2022] Open
Abstract
Hsp70 molecular chaperones play key roles in cellular protein homeostasis by binding to exposed hydrophobic regions of incompletely folded or aggregated proteins. This crucial Hsp70 function relies on allosteric communication between two well-structured domains: an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD), which are tethered by an interdomain linker. ATP or ADP binding to the NBD alters the substrate-binding affinity of the SBD, triggering functionally essential cycles of substrate binding and release. The interdomain linker is a well-structured participant in the interdomain interface in ATP-bound Hsp70s. By contrast, in the ADP-bound state, exemplified by the Escherichia coli Hsp70 DnaK, the interdomain linker is flexible. Hsp70 interdomain linker sequences are highly conserved; moreover, mutations in this region compromise interdomain allostery. To better understand the role of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformational landscape of the interdomain linker in ADP-bound DnaK and supported our simulations by strategic experimental data. We found that while the interdomain linker samples many conformations, it behaves as three relatively ordered segments connected by hinges. As a consequence, the distances and orientations between the NBD and SBD are limited. Additionally, the C-terminal region of the linker forms previously unreported, transient interactions with the SBD, and the predominant linker-docking site is available in only one allosteric state, that with high affinity for substrate. This preferential binding implicates the interdomain linker as a dynamic allosteric switch. The linker-binding site on the SBD is a potential target for small molecule modulators of the Hsp70 allosteric cycle.
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Affiliation(s)
| | - Woody Sherman
- From the Departments of Biochemistry and Molecular Biology and.,Schrödinger Inc., Cambridge, Massachusetts 02142.,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
| | - Wenli Meng
- From the Departments of Biochemistry and Molecular Biology and
| | - Lila M Gierasch
- From the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 and
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40
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Chan YH, Venev SV, Zeldovich KB, Matthews CR. Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints. Nat Commun 2017; 8:14614. [PMID: 28262665 PMCID: PMC5343507 DOI: 10.1038/ncomms14614] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/11/2017] [Indexed: 02/07/2023] Open
Abstract
Sequence divergence of orthologous proteins enables adaptation to environmental stresses and promotes evolution of novel functions. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Analysis of beneficial mutations pointed to an unexpected, long-range allosteric pathway towards the active site of the protein. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape and suggest that fitness landscapes can be translocated in sequence space. Exploration of fitness landscapes in the context of a protein fold provides a strategy for elucidating the sequence-structure-fitness relationships in other common motifs. The TIM barrel fold is an evolutionarily conserved motif found in proteins with a variety of enzymatic functions. Here the authors explore the fitness landscape of the TIM barrel protein IGPS and uncover evolutionary constraints on both sequence and structure, accompanied by long range allosteric interactions.
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Affiliation(s)
- Yvonne H Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
| | - Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, USA
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, USA
| | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
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41
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Hills RD, Brooks CL. Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci 2009; 10:889-905. [PMID: 19399227 PMCID: PMC2672008 DOI: 10.3390/ijms10030889] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 12/17/2022] Open
Abstract
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
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Affiliation(s)
- Ronald D. Hills
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
| | - Charles L. Brooks
- Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
- Department of Chemistry and Biophysics Program, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, USA
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +1-734-647-6682; Fax: +1-734-647-1604
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