1
|
Caba C, Black M, Liu Y, DaDalt AA, Mallare J, Fan L, Harding RJ, Wang Y, Vacratsis PO, Huang R, Zhuang Z, Tong Y. Autoinhibition of ubiquitin-specific protease 8: insights into domain interactions and mechanisms of regulation. J Biol Chem 2024:107727. [PMID: 39214302 DOI: 10.1016/j.jbc.2024.107727] [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: 05/30/2024] [Revised: 08/07/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Ubiquitin-specific proteases (USPs) are a family of multi-domain deubiquitinases (DUBs) with variable architectures, some containing regulatory auxiliary domains. Among the USP family, all occurrences of intramolecular regulation presently known are autoactivating. USP8 remains the sole exception as its putative WW-like domain, conserved only in vertebrate orthologs, is autoinhibitory. Here, we present a comprehensive structure-function analysis describing the autoinhibition of USP8 and provide evidence of the physical interaction between the WW-like and catalytic domains. The solution structure of full-length USP8 reveals an extended, monomeric conformation. Coupled with DUB assays, the WW-like domain is confirmed to be the minimal autoinhibitory unit. Strikingly, autoinhibition is only observed with the WW-like domain in cis and depends on the length of the linker tethering it to the catalytic domain. Modelling of the WW:CD complex structure and mutagenesis of interface residues suggests a novel binding site in the S1 pocket. To investigate the interplay between phosphorylation and USP8 autoinhibition, we identify AMP-activated protein kinase as a highly selective modifier of S718 in the 14-3-3 binding motif. We show that 14-3-3γ binding to phosphorylated USP8 potentiates autoinhibition in a WW-like domain-dependent manner by stabilizing an autoinhibited conformation. These findings provide mechanistic details on the autoregulation of USP8 and shed light on its evolutionary significance.
Collapse
Affiliation(s)
- Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, CAN N9B 3P4
| | - Megan Black
- Department of Chemistry, University of Guelph, Guelph, CAN N1G 2W1
| | - Yujue Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Ashley A DaDalt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, CAN N9B 3P4; Department of Biology, University of Michigan-Dearborn, Dearborn, MI 48128
| | - Josh Mallare
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, CAN N9B 3P4
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, CAN M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, CAN M5S 1A8
| | - Yunxin Wang
- Center for Structural Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702
| | | | - Rui Huang
- Department of Chemistry, University of Guelph, Guelph, CAN N1G 2W1
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, CAN N9B 3P4.
| |
Collapse
|
2
|
Dahiya D, Péter-Szabó Z, Senanayake M, Pingali SV, Leite WC, Byrnes J, Buchko GW, Sivan P, Vilaplana F, Master E, O'Neill H. SANS investigation of fungal loosenins reveal substrate dependent impacts of protein 1 action on inter-fibril distance and packing order of cellulosic substrates. RESEARCH SQUARE 2024:rs.3.rs-4769386. [PMID: 39184091 PMCID: PMC11343303 DOI: 10.21203/rs.3.rs-4769386/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
BACKGROUND Microbial expansin-related proteins include fungal loosenins, which have been previously shown to disrupt cellulose networks and enhance the enzymatic conversion of cellulosic substrates. Despite showing beneficial impacts to cellulose processing, detailed characterization of cellulosic materials after loosenin treatment is lacking. In this study, small-angle neutron scattering (SANS) was used to investigate the effects of three recombinantly produced loosenins that originate from Phanerochaete carnosa, PcaLOOL7, PcaLOOL9, and PcaLOOL12, on the organization of holocellulose preparations from Eucalyptus and Spruce wood samples. RESULTS Whereas the SANS analysis of Spruce holocellulose revealed an increase in interfibril spacing of neighboring cellulose microfibrils following treatment with PcaLOOL12 and to a lesser extent PcaLOOL7, the analysis of Eucalyptus holocellulose revealed a reduction in packing number following treatment with PcaLOOL12 and to a lesser extent PcaLOOL9. Parallel SEC-SAXS characterization of PcaLOOL7, PcaLOOL9, and PcaLOOL12 indicated the proteins likely function as monomers; moreover, all appear to retain a flexible disordered N-terminus and folded C-terminal region. The comparatively high impact of PcaLOOL12 motivated its NMR structural characterization, revealing a double-psi b-barrel (DPBB) domain surrounded by three alpha-helices - the largest nestled against the DPBB core and the other two part of loops extending from the core. CONCLUSIONS The SANS analysis of PcaLOOL action on holocellulose samples confirms their ability to disrupt cellulose fiber networks and suggests a progression from reducing microfibril packing to increasing interfibril distance. The most impactful PcaLOOL, PcaLOOL12, was previously observed to be the most highly expressed loosenin in P. carnosa. Its structural characterization herein reveals its stabilization through two disulfide linkages, and an extended N-terminal region distal to a negatively charged and surface accessible polysaccharide binding groove.
Collapse
|
3
|
Briganti L, Manzine LR, de Mello Capetti CC, de Araújo EA, de Oliveira Arnoldi Pellegrini V, Guimaraes FEG, de Oliveira Neto M, Polikarpov I. Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies. Int J Biol Macromol 2024; 274:133182. [PMID: 38885857 DOI: 10.1016/j.ijbiomac.2024.133182] [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: 12/23/2023] [Revised: 05/20/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Glycoside hydrolase family 5 (GH5) encompasses enzymes with several different activities, including endo-1,4-β-mannosidases. These enzymes are involved in mannan degradation, and have a number of biotechnological applications, such as mannooligosaccharide prebiotics production, stain removal and dyes decolorization, to name a few. Despite the importance of GH5 enzymes, only a few members of subfamily 7 were structurally characterized. In the present work, biochemical and structural characterization of Bacillus licheniformis GH5 mannanase, BlMan5_7 were performed and the enzyme cleavage pattern was analyzed, showing that BlMan5_7 requires at least 5 occupied subsites to perform efficient hydrolysis. Additionally, crystallographic structure at 1.3 Å resolution was determined and mannoheptaose (M7) was docked into the active site to investigate the interactions between substrate and enzyme through molecular dynamic (MD) simulations, revealing the existence of a - 4 subsite, which might explain the generation of mannotetraose (M4) as an enzyme product. Biotechnological application of the enzyme in stain removal was investigated, demonstrating that BlMan5_7 addition to washing solution greatly improves mannan-based stain elimination.
Collapse
Affiliation(s)
- Lorenzo Briganti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Livia R Manzine
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Caio Cesar de Mello Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | | | - Francisco Eduardo Gontijo Guimaraes
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Jr. s/n, Botucatu 18618-000, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil.
| |
Collapse
|
4
|
Shweta H, Gupta K, Zhou Y, Cui X, Li S, Lu Z, Goldman YE, Dantzig JA. Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein. RESEARCH SQUARE 2024:rs.3.rs-4638282. [PMID: 39070629 PMCID: PMC11276004 DOI: 10.21203/rs.3.rs-4638282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We present mCLIFY: a monomeric, bright, yellow, and long-lived fluorescent protein (FP) created by circular permutation of YPet, the brightest yellow FP from Aequorea Victoria for use in cellular and in vitro single molecule studies. mCLIFY retains the enhanced photophysical properties of YPET as a monomer at concentrations ≤ 40 μM. In contrast, we determined that YPet has a dimerization dissociation constant (K D 1-2) of 3.4 μM. Dimerization of YPet can cause homo-FRET, which underlies quantitative errors due to dimerization and homo-FRET. We determined the atomic structure of mCLIFY at 1.57 Å resolution and used its similarity with Venus for guided chromophore-targeted substitution studies to provide insights into its enhanced photophysical properties. The mutation V58L within the chromophore pocket improved quantum yield and extinction coefficient, making mCLIFY ~30% brighter than Venus. The extensive characterization of the photophysical and structural properties of YPet and mCLIFY presented here allowed us to reveal the basis of their long lifetimes and enhanced brightness and the basis of YPet's dimerization.
Collapse
Affiliation(s)
- Him Shweta
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Xiaonan Cui
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Selene Li
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yale E. Goldman
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Jody A. Dantzig
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| |
Collapse
|
5
|
Weaver GC, Schneider CL, Becerra-Artiles A, Clayton KL, Hudson AW, Stern LJ. The HHV-6B U20 glycoprotein binds ULBP1, masking it from recognition by NKG2D and interfering with natural killer cell activation. Front Immunol 2024; 15:1363156. [PMID: 38953028 PMCID: PMC11215065 DOI: 10.3389/fimmu.2024.1363156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction Human Herpesvirus 6B (HHV-6B) impedes host immune responses by downregulating class I MHC molecules (MHC-I), hindering antigen presentation to CD8+ T cells. Downregulation of MHC-I disengages inhibitory receptors on natural killer (NK) cells, resulting in activation and killing of the target cell if NK cell activating receptors such as NKG2D have engaged stress ligands upregulated on the target cells. Previous work has shown that HHV-6B downregulates three MHC-like stress ligands MICB, ULBP1, and ULBP3, which are recognized by NKG2D. The U20 glycoprotein of the related virus HHV-6A has been implicated in the downregulation of ULBP1, but the precise mechanism remains undetermined. Methods We set out to investigate the role of HHV-6B U20 in modulating NK cell activity. We used HHV-6B U20 expressed as a recombinant protein or transduced into target cells, as well as HHV-6B infection, to investigate binding interactions with NK cell ligands and receptors and to assess effects on NK cell activation. Small-angle X-ray scattering was used to align molecular models derived from machine-learning approaches. Results We demonstrate that U20 binds directly to ULBP1 with sub-micromolar affinity. Transduction of U20 decreases NKG2D binding to ULBP1 at the cell surface but does not decrease ULBP1 protein levels, either at the cell surface or in toto. HHV-6B infection and soluble U20 have the same effect. Transduction of U20 blocks NK cell activation in response to cell-surface ULBP1. Structural modeling of the U20 - ULBP1 complex indicates some similarities to the m152-RAE1γ complex.
Collapse
Affiliation(s)
- Grant C. Weaver
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, United States
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
| | - Christine L. Schneider
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | - Kiera L. Clayton
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, United States
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
| | - Amy W. Hudson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Lawrence J. Stern
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, United States
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, United States
| |
Collapse
|
6
|
Christensen NJ. Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations. PLoS One 2024; 19:e0293786. [PMID: 38718010 PMCID: PMC11078433 DOI: 10.1371/journal.pone.0293786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/25/2024] [Indexed: 05/12/2024] Open
Abstract
α-zeins are amphiphilic maize seed storage proteins with material properties suitable for a multitude of applications e.g., in renewable plastics, foods, therapeutics and additive manufacturing (3D-printing). To exploit their full potential, molecular-level insights are essential. The difficulties in experimental atomic-resolution characterization of α-zeins have resulted in a diversity of published molecular models. However, deep-learning α-zein models are largely unexplored. Therefore, this work studies an AlphaFold2 (AF2) model of a highly expressed α-zein using molecular dynamics (MD) simulations. The sequence of the α-zein cZ19C2 gave a loosely packed AF2 model with 7 α-helical segments connected by turns/loops. Compact tertiary structure was limited to a C-terminal bundle of three α-helices, each showing notable agreement with a published consensus sequence. Aiming to chart possible α-zein conformations in practically relevant solvents, rather than the native solid-state, the AF2 model was subjected to MD simulations in water/ethanol mixtures with varying ethanol concentrations. Despite giving structurally diverse endpoints, the simulations showed several patterns: In water and low ethanol concentrations, the model rapidly formed compact globular structures, largely preserving the C-terminal bundle. At ≥ 50 mol% ethanol, extended conformations prevailed, consistent with previous SAXS studies. Tertiary structure was partially stabilized in water and low ethanol concentrations, but was disrupted in ≥ 50 mol% ethanol. Aggregated results indicated minor increases in helicity with ethanol concentration. β-sheet content was consistently low (∼1%) across all conditions. Beyond structural dynamics, the rapid formation of branched α-zein aggregates in aqueous environments was highlighted. Furthermore, aqueous simulations revealed favorable interactions between the protein and the crosslinking agent glycidyl methacrylate (GMA). The proximity of GMA epoxide carbons and side chain hydroxyl oxygens simultaneously suggested accessible reactive sites in compact α-zein conformations and pre-reaction geometries for methacrylation. The findings may assist in expanding the applications of these technologically significant proteins, e.g., by guiding chemical modifications.
Collapse
|
7
|
De Caro L, Stoll T, Grandeury A, Gozzo F, Giannini C. Characterization of Surfactant Spheroidal Micelle Structure for Pharmaceutical Applications: A Novel Analytical Framework. Pharmaceutics 2024; 16:604. [PMID: 38794266 PMCID: PMC11125155 DOI: 10.3390/pharmaceutics16050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
We introduce an innovative theoretical framework tailored for the analysis of Pair Distribution Function (PDF) data derived from Small-Angle X-ray Scattering (SAXS) measurements of core-shell micelles. The new approach involves the exploitation of the first derivative of the PDF and the derivation of analytical equations to solve the core-shell micelle structure under the hypothesis of a spheroidal shape. These analytical equations enable us to determine the micelle's aggregation number, degree of ellipticity, and contrast in electron density between the core-shell and shell-buffer regions after having determined the whole micelle size and its shell size from the analysis of the first derivative of the PDF. We have formulated an overdetermined system of analytical equations based on the unknowns that characterize the micelle structure. This allows us to establish a Figure of Merit, which is utilized to identify the most reliable solution within the system of equations.
Collapse
Affiliation(s)
- Liberato De Caro
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70125 Bari, Italy;
| | - Thibaud Stoll
- Excelsus Structural Solutions (Swiss) AG, Park Innovaare, Parkstrasse 1, 5234 Villigen, Switzerland; (T.S.); (F.G.)
| | - Arnaud Grandeury
- Novartis Pharma AG, Technical Research and Development, Material Science, Novartis Campus, Virchow 6.3.231, 4056 Basel, Switzerland;
| | - Fabia Gozzo
- Excelsus Structural Solutions (Swiss) AG, Park Innovaare, Parkstrasse 1, 5234 Villigen, Switzerland; (T.S.); (F.G.)
| | - Cinzia Giannini
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70125 Bari, Italy;
| |
Collapse
|
8
|
Tamilselvan E, Sotomayor M. CELSR1, a core planar cell polarity protein, features a weakly adhesive and flexible cadherin ectodomain. Structure 2024; 32:476-491.e5. [PMID: 38307021 DOI: 10.1016/j.str.2024.01.003] [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: 05/14/2023] [Revised: 09/30/2023] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Planar cell polarity (PCP), essential to multicellular developmental processes, arises when cells polarize and align across tissues. Central to PCP is CELSR1, an atypical cadherin featuring a long ectodomain with nine extracellular cadherin (EC) repeats, a membrane adjacent domain (MAD10), and several characteristic adhesion GPCR domains. Cell-based aggregation assays have demonstrated CELSR1's homophilic adhesive nature, but mechanistic details are missing. Here, we investigate the possible adhesive properties and structures of CELSR1 EC repeats. Our bead aggregation assays do not support strong adhesion by EC repeats alone. Consistently, EC1-4 only dimerizes at high concentration in solution. Crystal structures of human CELSR1 EC1-4 and EC4-7 reveal typical folds and a non-canonical linker between EC5 and EC6. Simulations and experiments using EC4-7 indicate flexibility at EC5-6, and solution experiments show EC7-MAD10-mediated dimerization. Our results suggest weak homophilic adhesion by CELSR1 cadherin repeats and provide mechanistic insights into the structural determinants of CELSR1 function.
Collapse
Affiliation(s)
- Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
9
|
Vela‐Rodríguez C, Yang C, Alanen HI, Eki R, Abbas TA, Maksimainen MM, Glumoff T, Duman R, Wagner A, Paschal BM, Lehtiö L. Oligomerization mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor. Protein Sci 2024; 33:e4945. [PMID: 38511494 PMCID: PMC10955461 DOI: 10.1002/pro.4945] [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: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Deltex proteins are a family of E3 ubiquitin ligases that encode C-terminal RING and DTC domains that mediate interactions with E2 ubiquitin-conjugating enzymes and recognize ubiquitination substrates. DTX3L is unique among the Deltex proteins based on its N-terminal domain architecture. The N-terminal D1 and D2 domains of DTX3L mediate homo-oligomerization, and the D3 domain interacts with PARP9, a protein that contains tandem macrodomains with ADP-ribose reader function. While DTX3L and PARP9 are known to heterodimerize, and assemble into a high molecular weight oligomeric complex, the nature of the oligomeric structure, including whether this contributes to the ADP-ribose reader function is unknown. Here, we report a crystal structure of the DTX3L N-terminal D2 domain and show that it forms a tetramer with, conveniently, D2 symmetry. We identified two interfaces in the structure: a major, conserved interface with a surface of 973 Å2 and a smaller one of 415 Å2. Using native mass spectrometry, we observed molecular species that correspond to monomers, dimers and tetramers of the D2 domain. Reconstitution of DTX3L knockout cells with a D1-D2 deletion mutant showed the domain is dispensable for DTX3L-PARP9 heterodimer formation, but necessary to assemble an oligomeric complex with efficient reader function for ADP-ribosylated androgen receptor. Our results suggest that homo-oligomerization of DTX3L is important for the DTX3L-PARP9 complex to read mono-ADP-ribosylation on a ligand-regulated transcription factor.
Collapse
Affiliation(s)
- Carlos Vela‐Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Chunsong Yang
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heli I. Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Rebeka Eki
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Tarek A. Abbas
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Bryce M. Paschal
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| |
Collapse
|
10
|
Bories P, Rima J, Tranier S, Marcoux J, Grimoire Y, Tomaszczyk M, Launay A, Fata K, Marrakchi H, Burlet‐Schiltz O, Mourey L, Ducoux‐Petit M, Bardou F, Bon C, Quémard A. HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function. Protein Sci 2024; 33:e4964. [PMID: 38501584 PMCID: PMC10949391 DOI: 10.1002/pro.4964] [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: 11/21/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Worldwide, tuberculosis is the second leading infectious killer and multidrug resistance severely hampers disease control. Mycolic acids are a unique category of lipids that are essential for viability, virulence, and persistence of the causative agent, Mycobacterium tuberculosis (Mtb). Therefore, enzymes involved in mycolic acid biosynthesis represent an important class of drug targets. We previously showed that the (3R)-hydroxyacyl-ACP dehydratase (HAD) protein HadD is dedicated mainly to the production of ketomycolic acids and plays a determinant role in Mtb biofilm formation and virulence. Here, we discovered that HAD activity requires the formation of a tight heterotetramer between HadD and HadB, a HAD unit encoded by a distinct chromosomal region. Using biochemical, structural, and cell-based analyses, we showed that HadB is the catalytic subunit, whereas HadD is involved in substrate binding. Based on HadBDMtb crystal structure and substrate-bound models, we identified determinants of the ultra-long-chain lipid substrate specificity and revealed details of structure-function relationship. HadBDMtb unique function is partly due to a wider opening and a higher flexibility of the substrate-binding crevice in HadD, as well as the drastically truncated central α-helix of HadD hotdog fold, a feature described for the first time in a HAD enzyme. Taken together, our study shows that HadBDMtb , and not HadD alone, is the biologically relevant functional unit. These results have important implications for designing innovative antivirulence molecules to fight tuberculosis, as they suggest that the target to consider is not an isolated subunit, but the whole HadBD complex.
Collapse
Affiliation(s)
- Pascaline Bories
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Julie Rima
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Yasmina Grimoire
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Mathilde Tomaszczyk
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Anne Launay
- Service de TP de BiochimieUniversité de Toulouse, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Karine Fata
- Service de TP de BiochimieUniversité de Toulouse, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Odile Burlet‐Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Manuelle Ducoux‐Petit
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Fabienne Bardou
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| |
Collapse
|
11
|
Chandravanshi K, Singh R, Bhange GN, Kumar A, Yadav P, Kumar A, Makde RD. Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Lett 2024; 598:684-701. [PMID: 38426217 DOI: 10.1002/1873-3468.14834] [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: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Acylaminoacyl peptidases (AAPs) play a pivotal role in various pathological conditions and are recognized as potential therapeutic targets. AAPs exhibit a wide range of activities, such as acylated amino acid-dependent aminopeptidase, endopeptidase, and less studied carboxypeptidase activity. We have determined the crystal structure of an AAP from Geobacillus stearothermophilus (S9gs) at 2.0 Å resolution. Despite being annotated as an aminopeptidase in the NCBI database, our enzymatic characterization proved S9gs to be a carboxypeptidase. Solution-scattering studies showed that S9gs exists as a tetramer in solution, and crystal structure analysis revealed adaptations responsible for the carboxypeptidase activity of S9gs. The findings present a hypothesis for substrate selection, substrate entry, and product exit from the active site, enriching our understanding of this rare carboxypeptidase.
Collapse
Affiliation(s)
| | - Rahul Singh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Gauri N Bhange
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Amit Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| |
Collapse
|
12
|
Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [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: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
Collapse
Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| |
Collapse
|
13
|
Priest JM, Nichols EL, Smock RG, Hopkins JB, Mendoza JL, Meijers R, Shen K, Özkan E. Structural insights into the formation of repulsive netrin guidance complexes. SCIENCE ADVANCES 2024; 10:eadj8083. [PMID: 38363837 PMCID: PMC10871540 DOI: 10.1126/sciadv.adj8083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
Netrins dictate attractive and repulsive responses during axon growth and cell migration, where the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. Here, we showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5-heparin affinity using a directed evolution platform or structure-based rational design. We demonstrated that UNC-5 and UNC-6/netrin form a large, stable, and rigid complex in the presence of heparin, and heparin and UNC-5 exclude the attractive UNC-40/DCC receptor from binding to UNC-6/netrin to a large extent. Caenorhabditis elegans with a heparin-binding-deficient UNC-5 fail to establish proper gonad morphology due to abrogated cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Combining UNC-5 mutations targeting heparin and UNC-6/netrin contacts results in complete cell migration and axon guidance defects. Our findings establish repulsive netrin responses to be mediated through a glycosaminoglycan-regulated macromolecular complex.
Collapse
Affiliation(s)
- Jessica M. Priest
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Institute for Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Ev L. Nichols
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert G. Smock
- European Molecular Biology Laboratory (EMBL), Hamburg Site, c/o DESY, 22603 Hamburg, Germany
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Argonne National Laboratory, Illinois Institute of Technology, Chicago, IL 60616, USA
- Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Juan L. Mendoza
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Site, c/o DESY, 22603 Hamburg, Germany
- Institute for Protein Innovation (IPI), Boston, MA 02115, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Institute for Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
14
|
Rasal TA, Mallery CP, Brockley MW, Brown LC, Paczkowski JE, van Kessel JC. Ligand binding determines proteolytic stability of Vibrio LuxR/HapR quorum sensing transcription factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580527. [PMID: 38405947 PMCID: PMC10888775 DOI: 10.1101/2024.02.15.580527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In Vibrio species, quorum sensing signaling culminates in the production of a TetR-type master transcription factor collectively called the LuxR/HapR family, which regulates genes required for colonization and infection of host organisms. These proteins possess a solvent accessible putative ligand binding pocket. However, a native ligand has not been identified, and the role of ligand binding in LuxR/HapR function in Vibrionaceae is unknown. To probe the role of the ligand binding pocket, we utilize the small molecule thiophenesulfonamide inhibitor PTSP (3- p henyl-1-( t hiophen-2-yl s ulfonyl)-1 H - p yrazole) that we previously showed targets LuxR/HapR proteins. Amino acid conservation in the ligand binding pocket determines the specificity and efficacy of PTSP inhibition across Vibrio species. Here, we used structure-function analyses to identify PTSP-interacting residues in the ligand binding pocket of SmcR - the Vibrio vulnificus LuxR/HapR homolog - that are required for PTSP inhibition of SmcR activity in vivo . Forward genetic screening combined with X-ray crystallography structural determination of SmcR bound to PTSP identified substitutions at eight residues that were sufficient to reduce or eliminate PTSP-mediated SmcR inhibition. Small-angle X-ray scattering and computational modeling determined that PTSP drives allosteric unfolding at the N-terminal DNA binding domain. We discovered that SmcR is degraded by the ClpAP protease in the presence of PTSP in vivo ; substitution of key PTSP-interacting residues stabilized or increased SmcR levels in the cell. This mechanism of inhibition is observed for all thiophenesulfonamide compounds tested and against other Vibrio species. We conclude that thiophenesulfonamides specifically bind in the ligand binding pocket of LuxR/HapR proteins, promoting protein degradation and thereby suppressing downstream gene expression, implicating ligand binding as a mediator of LuxR/HapR protein stability and function to govern virulence gene expression in Vibrio pathogens. SIGNIFICANCE LuxR/HapR proteins were discovered in the 1990s as central regulators of quorum sensing gene expression and later discovered to be conserved in all studied Vibrio species. LuxR/HapR homologs regulate a wide range of genes involved in pathogenesis, including but not limited to genes involved in biofilm production and toxin secretion. As archetypal members of the broad class of TetR-type transcription factors, each LuxR/HapR protein has a predicted ligand binding pocket. However, no ligand has been identified for LuxR/HapR proteins that control their function as regulators. Here, we used LuxR/HapR-specific chemical inhibitors to determine that ligand binding drives proteolytic degradation in vivo , the first demonstration of LuxR/HapR function connected to ligand binding for this historical protein family.
Collapse
|
15
|
Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
Collapse
Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
16
|
Hopkins JB. BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis. J Appl Crystallogr 2024; 57:194-208. [PMID: 38322719 PMCID: PMC10840314 DOI: 10.1107/s1600576723011019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and D max finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.
Collapse
Affiliation(s)
- Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| |
Collapse
|
17
|
Geens R, Stanisich J, Beyens O, D'Hondt S, Thiberge J, Ryckebosch A, De Groot A, Magez S, Vertommen D, Amino R, De Winter H, Volkov AN, Tompa P, Sterckx YG. Biophysical characterization of the Plasmodium falciparum circumsporozoite protein's N-terminal domain. Protein Sci 2024; 33:e4852. [PMID: 38059674 PMCID: PMC10749493 DOI: 10.1002/pro.4852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
The circumsporozoite protein (CSP) is the main surface antigen of the Plasmodium sporozoite (SPZ) and forms the basis of the currently only licensed anti-malarial vaccine (RTS,S/AS01). CSP uniformly coats the SPZ and plays a pivotal role in its immunobiology, in both the insect and the vertebrate hosts. Although CSP's N-terminal domain (CSPN ) has been reported to play an important role in multiple CSP functions, a thorough biophysical and structural characterization of CSPN is currently lacking. Here, we present an alternative method for the recombinant production and purification of CSPN from Plasmodium falciparum (PfCSPN ), which provides pure, high-quality protein preparations with high yields. Through an interdisciplinary approach combining in-solution experimental methods and in silico analyses, we provide strong evidence that PfCSPN is an intrinsically disordered region displaying some degree of compaction.
Collapse
Affiliation(s)
- Rob Geens
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Jessica Stanisich
- Cellular and Molecular ImmunologyVrije Universiteit BrusselBrusselsBelgium
| | - Olivier Beyens
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | - Stijn D'Hondt
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | | | - Amber Ryckebosch
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
| | - Anke De Groot
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
| | - Stefan Magez
- Cellular and Molecular ImmunologyVrije Universiteit BrusselBrusselsBelgium
- Ghent University Global CampusIncheonSouth Korea
| | - Didier Vertommen
- de Duve Institute and MASSPROT Platform, UCLouvainBrusselsBelgium
| | - Rogerio Amino
- Unit of Malaria Infection & ImmunityInstitut PasteurParisFrance
| | - Hans De Winter
- Laboratory of Medicinal Chemistry (UAMC)University of AntwerpAntwerpBelgium
| | - Alexander N. Volkov
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor Biotechnologie (VIB)BrusselsBelgium
- Jean Jeener NMR CentreVrije Universiteit BrusselBrusselsBelgium
| | - Peter Tompa
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor Biotechnologie (VIB)BrusselsBelgium
- Institute of Enzymology, Biological Research CenterHungarian Academy of SciencesBudapestHungary
| | - Yann G.‐J. Sterckx
- Laboratory of Medical Biochemistry (LMB)University of AntwerpAntwerpBelgium
| |
Collapse
|
18
|
Arriaza RH, Abiskaroon B, Patel M, Daneshian L, Kluza A, Snoeck S, Watkins MB, Hopkins JB, Van Leeuwen T, Grbic M, Grbic V, Borowski T, Chruszcz M. Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest. J Biol Chem 2023; 299:105421. [PMID: 37923139 PMCID: PMC10731231 DOI: 10.1016/j.jbc.2023.105421] [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: 09/18/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for UDP glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism; however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site-directed mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor-binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.
Collapse
Affiliation(s)
- Ricardo Hernandez Arriaza
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Brendan Abiskaroon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Megha Patel
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Krakow, Poland
| | - Simon Snoeck
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario, Canada; University of La Rioja, Logrono, Spain
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario, Canada
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Krakow, Poland
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA.
| |
Collapse
|
19
|
Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [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: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
Collapse
Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| |
Collapse
|
20
|
Vela-Rodríguez C, Yang C, Alanen HI, Eki R, Abbas TA, Maksimainen MM, Glumoff T, Duman R, Wagner A, Paschal BM, Lehtiö L. Oligomerisation mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569193. [PMID: 38076829 PMCID: PMC10705365 DOI: 10.1101/2023.11.29.569193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Deltex proteins are a family of E3 ubiquitin ligases that encode C-terminal RING and DTC domains that mediate interactions with E2 ubiquitin-conjugating enzymes and recognise ubiquitination substrates. DTX3L is unique among the Deltex proteins based on its N-terminal domain architecture. The N-terminal D1 and D2 domains of DTX3L mediate homo-oligomerisation, and the D3 domain interacts with PARP9, a protein that contains tandem macrodomains with ADP-ribose reader function. While DTX3L and PARP9 are known to heterodimerize, they assemble into a high molecular weight oligomeric complex, but the nature of the oligomeric structure, including whether this contributes to the ADP-ribose reader function is unknown. Here, we report a crystal structure of the DTX3L N-terminal D2 domain and show that it forms a tetramer with, conveniently, D2 symmetry. We identified two interfaces in the structure: a major, conserved interface with a surface of 973 Å2 and a smaller one of 415 Å2. Using native mass spectrometry, we observed molecular species that correspond to monomers, dimers and tetramers of the D2 domain. Reconstitution of DTX3L knockout cells with a D1-D2 deletion mutant showed the domain is dispensable for DTX3L-PARP9 heterodimer formation, but necessary to assemble an oligomeric complex with efficient reader function for ADP-ribosylated androgen receptor. Our results suggest that homo-oligomerisation of DTX3L is important for mono-ADP-ribosylation reading by the DTX3L-PARP9 complex and to a ligand-regulated transcription factor.
Collapse
Affiliation(s)
- Carlos Vela-Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Chunsong Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia, USA
| | - Heli I. Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Rebeka Eki
- Department of Radiation Oncology, University of Virginia, USA
| | - Tarek A. Abbas
- Department of Radiation Oncology, University of Virginia, USA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Bryce M. Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, USA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| |
Collapse
|
21
|
Ogbu CP, Kapoor S, Vecchio AJ. Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin. Toxins (Basel) 2023; 15:637. [PMID: 37999500 PMCID: PMC10674488 DOI: 10.3390/toxins15110637] [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: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin's role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.
Collapse
Affiliation(s)
| | | | - Alex J. Vecchio
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY 14203, USA; (C.P.O.); (S.K.)
| |
Collapse
|
22
|
Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
Collapse
Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
23
|
Pierson E, De Pol F, Fillet M, Wouters J. A morpheein equilibrium regulates catalysis in phosphoserine phosphatase SerB2 from Mycobacterium tuberculosis. Commun Biol 2023; 6:1024. [PMID: 37817000 PMCID: PMC10564941 DOI: 10.1038/s42003-023-05402-z] [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: 02/13/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Mycobacterium tuberculosis phosphoserine phosphatase MtSerB2 is of interest as a new antituberculosis target due to its essential metabolic role in L-serine biosynthesis and effector functions in infected cells. Previous works indicated that MtSerB2 is regulated through an oligomeric transition induced by L-Ser that could serve as a basis for the design of selective allosteric inhibitors. However, the mechanism underlying this transition remains highly elusive due to the lack of experimental structural data. Here we describe a structural, biophysical, and enzymological characterisation of MtSerB2 oligomerisation in the presence and absence of L-Ser. We show that MtSerB2 coexists in dimeric, trimeric, and tetrameric forms of different activity levels interconverting through a conformationally flexible monomeric state, which is not observed in two near-identical mycobacterial orthologs. This morpheein behaviour exhibited by MtSerB2 lays the foundation for future allosteric drug discovery and provides a starting point to the understanding of its peculiar multifunctional moonlighting properties.
Collapse
Affiliation(s)
- Elise Pierson
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Florian De Pol
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Center for Interdisciplinary Research on Medicines (CIRM), University of Liège (ULiège), 4000, Liège, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium.
| |
Collapse
|
24
|
Vish KJ, Stiegler AL, Boggon TJ. Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP, and Dok1. J Biol Chem 2023; 299:105098. [PMID: 37507023 PMCID: PMC10470053 DOI: 10.1016/j.jbc.2023.105098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023] Open
Abstract
RasGAP (p120RasGAP), the founding member of the GTPase-activating protein (GAP) family, is one of only nine human proteins to contain two SH2 domains and is essential for proper vascular development. Despite its importance, its interactions with key binding partners remains unclear. In this study we provide a detailed viewpoint of RasGAP recruitment to various binding partners and assess their impact on RasGAP activity. We reveal the RasGAP SH2 domains generate distinct binding interactions with three well-known doubly phosphorylated binding partners: p190RhoGAP, Dok1, and EphB4. Affinity measurements demonstrate a 100-fold weakened affinity for RasGAP-EphB4 binding compared to RasGAP-p190RhoGAP or RasGAP-Dok1 binding, possibly driven by single versus dual SH2 domain engagement with a dominant N-terminal SH2 interaction. Small-angle X-ray scattering reveals conformational differences between RasGAP-EphB4 binding and RasGAP-p190RhoGAP binding. Importantly, these interactions do not impact catalytic activity, implying RasGAP utilizes its SH2 domains to achieve diverse spatial-temporal regulation of Ras signaling in a previously unrecognized fashion.
Collapse
Affiliation(s)
- Kimberly J Vish
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Pharmacology, Yale University, New Haven, Connecticut, USA; Department of Yale Cancer Center, Yale University, New Haven, Connecticut, USA.
| |
Collapse
|
25
|
McKay CE, Cheng J, Tanner JJ. Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold. Sci Rep 2023; 13:13496. [PMID: 37596303 PMCID: PMC10439177 DOI: 10.1038/s41598-023-40558-y] [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: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C2221 and P3221) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11-57 and 102-148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.
Collapse
Affiliation(s)
- Cole E McKay
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
26
|
Blanc M, Lettl C, Guérin J, Vieille A, Furler S, Briand-Schumacher S, Dreier B, Bergé C, Plückthun A, Vadon-Le Goff S, Fronzes R, Rousselle P, Fischer W, Terradot L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 2023; 19:e1011368. [PMID: 37155700 DOI: 10.1371/journal.ppat.1011368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/18/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The bacterial human pathogen Helicobacter pylori produces a type IV secretion system (cagT4SS) to inject the oncoprotein CagA into gastric cells. The cagT4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shape N-terminal domains (CagIN) prolonged by globular C-terminal domains (CagIC). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagIC with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagIC were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagIC plays a key role in cagT4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cagT4SS, a crucial risk factor for gastric cancer development.
Collapse
Affiliation(s)
- Marine Blanc
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jérémy Guérin
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Anaïs Vieille
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Sven Furler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Rémi Fronzes
- European Institute of Chemistry and Biology, CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Univ. Bordeaux, Pessac, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| |
Collapse
|
27
|
Annamraju A, Rajan K, Zuo X, Long BK, Pingali SV, Elder TJ, Labbé N. Atomic Level Interactions and Suprastructural Configuration of Plant Cell Wall Polymers in Dialkylimidazolium Ionic Liquids. Biomacromolecules 2023; 24:2164-2172. [PMID: 36977326 DOI: 10.1021/acs.biomac.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Ionic liquids (ILs) have been widely investigated for the pretreatment and deconstruction of lignocellulosic feedstocks. However, the modes of interaction between IL-anions and cations, and plant cell wall polymers, namely, cellulose, hemicellulose, and lignin, as well as the resulting ultrastructural changes are still unclear. In this study, we investigated the atomic level and suprastructural interactions of microcrystalline cellulose, birchwood xylan, and organosolv lignin with 1,3-dialkylimidazolium ILs having varying sizes of carboxylate anions. Analysis by 13C NMR spectroscopy indicated that cellulose and lignin exhibited stronger hydrogen bonding with acetate ions than with formate ions, as evidenced by greater chemical shift changes. Small-angle X-ray scattering analysis showed that while both cellulose and xylan adopted a single-stranded conformation in acetate-ILs, twice as many acetate ions were bound to one anhydroglucose unit than to an anhydroxylose unit. We also determined that a minimum of seven representative carbohydrate units must interact with an anion for that IL to effectively dissolve cellulose or xylan. Lignin is associated as groups of four polymer molecules in formate-ILs and dispersed as single molecules in acetate-ILs, which indicates that it is highly soluble in the latter. In summary, our study demonstrated that 1,3-dialkylimidazolium acetates displayed stronger binding interactions with cellulose and lignin, as compared to formates, and thus have superior potential to fractionate these polymers from lignocellulosic feedstocks.
Collapse
Affiliation(s)
| | | | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Brian K Long
- Department of Chemistry, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Thomas J Elder
- USDA-Forest Service, Southern Research Station, Auburn, Alabama 36849, United States
| | | |
Collapse
|
28
|
Batista M, Donker EIM, Bon C, Guillien M, Caisso A, Mourey Funding L, Marie François Funding J, Maveyraud L, Zerbib D. The conserved yeast protein Knr4 involved in cell wall integrity is a multi-domain intrinsically disordered protein. J Mol Biol 2023; 435:168048. [PMID: 36933821 DOI: 10.1016/j.jmb.2023.168048] [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: 10/26/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Knr4/Smi1 proteins are specific to the fungal kingdom and their deletion in the model yeast Saccharomyces cerevisiae and the human pathogen Candida albicans results in hypersensitivity to specific antifungal agents and a wide range of parietal stresses. In S. cerevisiae, Knr4 is located at the crossroads of several signalling pathways, including the conserved cell wall integrity and calcineurin pathways. Knr4 interacts genetically and physically with several protein members of those pathways. Its sequence suggests that it contains large intrinsically disordered regions. Here, a combination of small-angle X-ray scattering (SAXS) and crystallographic analysis led to a comprehensive structural view of Knr4. This experimental work unambiguously showed that Knr4 comprises two large intrinsically disordered regions flanking a central globular domain whose structure has been established. The structured domain is itself interrupted by a disordered loop. Using the CRISPR/Cas9 genome editing technique, strains expressing KNR4 genes deleted from different domains were constructed. The N-terminal domain and the loop are essential for optimal resistance to cell wall-binding stressors. The C-terminal disordered domain, on the other hand, acts as a negative regulator of this function of Knr4. The identification of molecular recognition features, the possible presence of secondary structure in these disordered domains and the functional importance of the disordered domains revealed here designate these domains as putative interacting spots with partners in either pathway. Targeting these interacting regions is a promising route to the discovery of inhibitory molecules that could increase the susceptibility of pathogens to the antifungals currently in clinical use.
Collapse
Affiliation(s)
- Manon Batista
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Ellen I M Donker
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Myriam Guillien
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Adriana Caisso
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France
| | - Lionel Mourey Funding
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France.
| | - Didier Zerbib
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France.
| |
Collapse
|
29
|
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res 2023; 51:1674-1686. [PMID: 36660822 PMCID: PMC9976917 DOI: 10.1093/nar/gkac1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/19/2022] [Accepted: 12/27/2022] [Indexed: 01/21/2023] Open
Abstract
ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.
Collapse
Affiliation(s)
- Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu Cao
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chenxi He
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xianjiang Lan
- Department of Systems Biology for Medicine, School of Basic Medical Sciences; Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Division of Hematology, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gerd A Blobel
- Division of Hematology, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
30
|
Marchenkov V, Ivashina T, Marchenko N, Ryabova N, Selivanova O, Timchenko A, Kihara H, Ksenzenko V, Semisotnov G. In Vivo Incorporation of Photoproteins into GroEL Chaperonin Retaining Major Structural and Functional Properties. Molecules 2023; 28:molecules28041901. [PMID: 36838891 PMCID: PMC9965216 DOI: 10.3390/molecules28041901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The incorporation of photoproteins into proteins of interest allows the study of either their localization or intermolecular interactions in the cell. Here we demonstrate the possibility of in vivo incorporating the photoprotein Aequorea victoria enhanced green fluorescent protein (EGFP) or Gaussia princeps luciferase (GLuc) into the tetradecameric quaternary structure of GroEL chaperonin and describe some physicochemical properties of the labeled chaperonin. Using size-exclusion and affinity chromatography, electrophoresis, fluorescent and electron transmission microscopy (ETM), small-angle X-ray scattering (SAXS), and bioluminescence resonance energy transfer (BRET), we show the following: (i) The GroEL14-EGFP is evenly distributed within normally divided E. coli cells, while gigantic undivided cells are characterized by the uneven distribution of the labeled GroEL14 which is mainly localized close to the cellular periplasm; (ii) EGFP and likely GLuc are located within the inner cavity of one of the two GroEL chaperonin rings and do not essentially influence the protein oligomeric structure; (iii) GroEL14 containing either EGFP or GLuc is capable of interacting with non-native proteins and the cochaperonin GroES.
Collapse
Affiliation(s)
- Victor Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Tanya Ivashina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, 142290 Pushchino, Russia
| | - Natalia Marchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Natalya Ryabova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Olga Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Alexander Timchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Hiroshi Kihara
- Department of Physics, Kansai Medical University, Shin-Machi 2-5-1, Hirakata 573-1010, Japan
| | - Vladimir Ksenzenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
| | - Gennady Semisotnov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya St., 142290 Pushchino, Russia
- Correspondence: ; Tel.: +7-(496)-731-8409
| |
Collapse
|
31
|
Trewhella J, Jeffries CM, Whitten AE. 2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data. Acta Crystallogr D Struct Biol 2023; 79:122-132. [PMID: 36762858 PMCID: PMC9912924 DOI: 10.1107/s2059798322012141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/23/2022] [Indexed: 02/10/2023] Open
Abstract
In 2017, guidelines were published for reporting structural modelling of small-angle scattering (SAS) data from biomolecules in solution that exemplified best-practice documentation of experiments and analysis. Since then, there has been significant progress in SAS data and model archiving, and the IUCr journal editors announced that the IUCr biology journals will require the deposition of SAS data used in biomolecular structure solution into a public archive, as well as adherence to the 2017 reporting guidelines. In this context, the reporting template tables accompanying the 2017 publication guidelines have been reviewed with a focus on making them both easier to use and more general. With input from the SAS community via the IUCr Commission on SAS and attendees of the triennial 2022 SAS meeting (SAS2022, Campinas, Brazil), an updated reporting template table has been developed that includes standard descriptions for proteins, glycosylated proteins, DNA and RNA, with some reorganization of the data to improve readability and interpretation. In addition, a specialized template has been developed for reporting SAS contrast-variation (SAS-cv) data and models that incorporates the additional reporting requirements from the 2017 guidelines for these more complicated experiments. To demonstrate their utility, examples of reporting with these new templates are provided for a SAS study of a DNA-protein complex and a SAS-cv experiment on a protein complex. The examples demonstrate how the tabulated information promotes transparent reporting that, in combination with the recommended figures and additional information best presented in the main text, enables the reader of the work to readily draw their own conclusions regarding the quality of the data and the validity of the models presented.
Collapse
Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| |
Collapse
|
32
|
Santos JC, Handa S, Fernandes LGV, Bleicher L, Gandin CA, de Oliveira-Neto M, Ghosh P, Nascimento ALTO. Structural and biochemical characterization of Leptospira interrogans Lsa45 reveals a penicillin-binding protein with esterase activity. Process Biochem 2023; 125:141-153. [PMID: 36643388 PMCID: PMC9836055 DOI: 10.1016/j.procbio.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Leptospirosis is a bacterial disease that affects humans and animals and is caused by Leptospira. The recommended treatment for leptospirosis is antibiotic therapy, which should be given early in the course of the disease. Despite the use of these antibiotics, their role during the course of the disease is still not completely clear because of the lack of effective clinical trials, particularly for severe cases of the disease. Here, we present the characterization of L. interrogans Lsa45 protein by gel filtration, protein crystallography, SAXS, fluorescence and enzymatic assays. The oligomeric studies revealed that Lsa45 is monomeric in solution. The crystal structure of Lsa45 revealed the presence of two subdomains: a large α/β subdomain and a small α-helical subdomain. The large subdomain contains the amino acids Ser122, Lys125, and Tyr217, which correspond to the catalytic triad that is essential for β-lactamase or serine hydrolase activity in similar enzymes. Additionally, we also confirmed the bifunctional promiscuity of Lsa45, in hydrolyzing both the 4-nitrophenyl acetate (p-NPA) and nitrocefin β-lactam antibiotic. Therefore, this study provides novel insights into the structure and function of enzymes from L. interrogans, which furthers our understanding of this bacterium and the development of new therapies for the prevention and treatment of leptospirosis.
Collapse
Affiliation(s)
- Jademilson C. Santos
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
- Instituto Federal da Bahia – IFBA - Rodovia BR-367, R. José Fontana, 1, 45810-000, Porto Seguro - BA, Brazil
| | - Sumit Handa
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Luis G. V. Fernandes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - César A. Gandin
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Dep. de Física e Biofísica, Botucatu, SP, Brazil
| | - Mario de Oliveira-Neto
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Dep. de Física e Biofísica, Botucatu, SP, Brazil
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Ana Lucia T. O. Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
| |
Collapse
|
33
|
Yadav R, Courouble VV, Dey SK, Harrison JJE, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E. Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. SCIENCE ADVANCES 2022; 8:eadd2191. [PMID: 36490335 PMCID: PMC9733933 DOI: 10.1126/sciadv.add2191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
Collapse
Affiliation(s)
- Ruchi Yadav
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - Sanjay K. Dey
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | | | - Jennifer Timm
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Ryan L. Slack
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
- Department of Molecular Medicine, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| |
Collapse
|
34
|
Wu Y, Huo C, Ming T, Liu Y, Su C, Qiu X, Lu C, Zhou J, Li Y, Zhang Z, Han J, Feng Y, Su X. Structural and Functional Insights into the Roles of Potential Metal-Binding Sites in Apostichopus japonicus Ferritin. Polymers (Basel) 2022; 14:5378. [PMID: 36559745 PMCID: PMC9785301 DOI: 10.3390/polym14245378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Ferritin is widely acknowledged as a conservative iron storage protein found in almost all living kingdoms. Apostichopus japonicus (Selenka) is among the oldest echinoderm fauna and has unique regenerative potential, but the catalytic mechanism of iron oxidation in A. japonicus ferritin (AjFER) remains elusive. We previously identified several potential metal-binding sites at the ferroxidase center, the three- and four-fold channels in AjFER. Herein, we prepared AjFER, AjFER-E25A/E60A/E105A, AjFER-D129A/E132A, and AjFER-E168A mutants, investigated their structures, and functionally characterized these ferritins with respect to Fe2+ uptake using X-ray techniques together with biochemical analytical methods. A crystallographic model of the AjFER-D129A/E132A mutant, which was solved to a resolution of 1.98 Å, suggested that the substitutions had a significant influence on the quaternary structure of the three-fold channel compared to that of AjFER. The structures of these ferritins in solution were determined based on the molecular envelopes of AjFER and its variants by small-angle X-ray scattering, and the structures were almost consistent with the characteristics of well-folded and globular-shaped proteins. Comparative biochemical analyses indicated that site-directed mutagenesis of metal-binding sites in AjFER presented relatively low rates of iron oxidation and thermostability, as well as weak iron-binding affinity, suggesting that these potential metal-binding sites play critical roles in the catalytic activity of ferritin. These findings provide profound insight into the structure-function relationships related to marine invertebrate ferritins.
Collapse
Affiliation(s)
- Yan Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Chunheng Huo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Yan Liu
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo 315800, China
| | - Chang Su
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo 315800, China
| | - Xiaoting Qiu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Ying Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- College of Life Sciences, Tonghua Normal University, Tonghua 134000, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| |
Collapse
|
35
|
Stiegler AL, Vish KJ, Boggon TJ. Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP. Structure 2022; 30:1603-1614.e5. [PMID: 36417908 PMCID: PMC9722645 DOI: 10.1016/j.str.2022.10.009] [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: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
p120RasGAP is a multidomain GTPase-activating protein for Ras. The presence of two Src homology 2 domains in an SH2-SH3-SH2 module raises the possibility that p120RasGAP simultaneously binds dual phosphotyrosine residues in target proteins. One known binding partner with two proximal phosphotyrosines is p190RhoGAP, a GTPase-activating protein for Rho GTPases. Here, we present the crystal structure of the p120RasGAP SH2-SH3-SH2 module bound to a doubly tyrosine-phosphorylated p190RhoGAP peptide, revealing simultaneous phosphotyrosine recognition by the SH2 domains. The compact arrangement places the SH2 domains in close proximity resembling an SH2 domain tandem and exposed SH3 domain. Affinity measurements support synergistic binding, while solution scattering reveals that dual phosphotyrosine binding induces compaction of this region. Our studies reflect a binding mode that limits conformational flexibility within the SH2-SH3-SH2 cassette and relies on the spacing and sequence surrounding the two phosphotyrosines, potentially representing a selectivity mechanism for downstream signaling events.
Collapse
Affiliation(s)
- Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Kimberly J Vish
- Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Cancer Center, Yale University, New Haven, CT, USA.
| |
Collapse
|
36
|
Miller RC, Cummings C, Huang Q, Ando N, Gillilan RE. Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure. Protein Sci 2022; 31:e4489. [PMID: 36320105 PMCID: PMC9669991 DOI: 10.1002/pro.4489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small-angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography-coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. The apparatus described here functions at a range of temperatures (0°C-50°C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.
Collapse
Affiliation(s)
- Robert C. Miller
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
| | - Cody Cummings
- Center for High Energy X‐ray Sciences (CHEXS)IthacaNew YorkUSA
| | - Qingqiu Huang
- Center for High Energy X‐ray Sciences (CHEXS)IthacaNew YorkUSA
| | - Nozomi Ando
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
| | | |
Collapse
|
37
|
Schmitz C, Madej M, Nowakowska Z, Cuppari A, Jacula A, Ksiazek M, Mikruta K, Wisniewski J, Pudelko-Malik N, Saran A, Zeytuni N, Mlynarz P, Lamont RJ, Usón I, Siksnys V, Potempa J, Solà M. Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors. Nucleic Acids Res 2022; 50:12558-12577. [PMID: 36464236 PMCID: PMC9757075 DOI: 10.1093/nar/gkac1103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022] Open
Abstract
The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.
Collapse
Affiliation(s)
- Claus Schmitz
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Anna Cuppari
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Anna Jacula
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Miroslaw Ksiazek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Katarzyna Mikruta
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Jerzy Wisniewski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Natalia Pudelko-Malik
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Anshu Saran
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Natalie Zeytuni
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Piotr Mlynarz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Isabel Usón
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
- ICREA Institució Catalana de Recerca i Estudis Avançats, Barcelona E-08010, Spain
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Maria Solà
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| |
Collapse
|
38
|
Bahraminejad E, Paliwal D, Sunde M, Holt C, Carver JA, Thorn DC. Amyloid fibril formation by α S1- and β-casein implies that fibril formation is a general property of casein proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140854. [PMID: 36087849 DOI: 10.1016/j.bbapap.2022.140854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Caseins are a diverse family of intrinsically disordered proteins present in the milks of all mammals. A property common to two cow paralogues, αS2- and κ-casein, is their propensity in vitro to form amyloid fibrils, the highly ordered protein aggregates associated with many age-related, including neurological, diseases. In this study, we explored whether amyloid fibril-forming propensity is a general feature of casein proteins by examining the other cow caseins (αS1 and β) as well as β-caseins from camel and goat. Small-angle X-ray scattering measurements indicated that cow αS1- and β-casein formed large spherical aggregates at neutral pH and 20°C. Upon incubation at 65°C, αS1- and β-casein underwent conversion to amyloid fibrils over the course of ten days, as shown by thioflavin T binding, transmission electron microscopy, and X-ray fibre diffraction. At the lower temperature of 37°C where fibril formation was more limited, camel β-casein exhibited a greater fibril-forming propensity than its cow or goat orthologues. Limited proteolysis of cow and camel β-casein fibrils and analysis by mass spectrometry indicated a common amyloidogenic sequence in the proline, glutamine-rich, C-terminal region of β-casein. These findings highlight the persistence of amyloidogenic sequences within caseins, which likely contribute to their functional, heterotypic self-assembly; in all mammalian milks, at least two caseins coalesce to form casein micelles, implying that caseins diversified partly to avoid dysfunctional amyloid fibril formation.
Collapse
Affiliation(s)
- Elmira Bahraminejad
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Devashi Paliwal
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Margaret Sunde
- School of Medical Sciences, Faculty of Medicine and Health, and Sydney Nano, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carl Holt
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - David C Thorn
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.
| |
Collapse
|
39
|
Mertens HDT. Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS. Methods Enzymol 2022; 678:193-236. [PMID: 36641208 DOI: 10.1016/bs.mie.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ATSAS software suite provides a comprehensive set of programs for the processing, analysis and modeling of small-angle scattering data, tailored for but not limited to data acquired on biological macromolecules. In this review the major components and developments in the ATSAS package are described, with a focus on user driven application. Data reduction, analysis and modeling approaches and strategies will be introduced and discussed. At the time of writing the latest package, ATSAS 3.1, is freely available for academic users at: https://www.embl-hamburg.de/biosaxs/software.html.
Collapse
|
40
|
Lyons NS, Bogner AN, Tanner JJ, Sobrado P. Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N-Hydroxylase from Acinetobacter baumannii. Biochemistry 2022; 61:2607-2620. [DOI: 10.1021/acs.biochem.2c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noah S. Lyons
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
41
|
Felix J, Bumba L, Liesche C, Fraudeau A, Rébeillé F, El Khoury JY, Huard K, Gallet B, Moriscot C, Kleman JP, Duhoo Y, Jessop M, Kandiah E, Barras F, Jouhet J, Gutsche I. The AAA+ ATPase RavA and its binding partner ViaA modulate E. coli aminoglycoside sensitivity through interaction with the inner membrane. Nat Commun 2022; 13:5502. [PMID: 36127320 PMCID: PMC9489729 DOI: 10.1038/s41467-022-32992-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Enteric bacteria have to adapt to environmental stresses in the human gastrointestinal tract such as acid and nutrient stress, oxygen limitation and exposure to antibiotics. Membrane lipid composition has recently emerged as a key factor for stress adaptation. The E. coli ravA-viaA operon is essential for aminoglycoside bactericidal activity under anaerobiosis but its mechanism of action is unclear. Here we characterise the VWA domain-protein ViaA and its interaction with the AAA+ ATPase RavA, and find that both proteins localise at the inner cell membrane. We demonstrate that RavA and ViaA target specific phospholipids and subsequently identify their lipid-binding sites. We further show that mutations abolishing interaction with lipids restore induced changes in cell membrane morphology and lipid composition. Finally we reveal that these mutations render E. coli gentamicin-resistant under fumarate respiration conditions. Our work thus uncovers a ravA-viaA-based pathway which is mobilised in response to aminoglycosides under anaerobiosis and engaged in cell membrane regulation.
Collapse
Affiliation(s)
- Jan Felix
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ladislav Bumba
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Institute of Microbiology, The Academy of Sciences of the Czech Republic, Videnska, 1083, Prague, Czech Republic
| | - Clarissa Liesche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Angélique Fraudeau
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- EMBL Grenoble, 71 Avenue des martyrs, Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Jessica Y El Khoury
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Karine Huard
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Christine Moriscot
- Univ Grenoble Alpes, CEA, CNRS, ISBG, 71 Avenue des martyrs, Grenoble, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Yoan Duhoo
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Eaazhisai Kandiah
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des martyrs, Grenoble, France
| | - Frédéric Barras
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France.
| |
Collapse
|
42
|
Pinto D, Gonçalo R, Louro M, Silva MS, Hernandez G, Cordeiro TN, Cordeiro C, São-José C. On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes. Microbiol Spectr 2022; 10:e0103722. [PMID: 35876588 PMCID: PMC9430671 DOI: 10.1128/spectrum.01037-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages (phages) and other viruses are extremely efficient in packing their genetic information, with several described cases of overlapping genes encoded in different open reading frames (ORFs). While less frequently reported, specific cases exist in which two overlapping ORFs are in frame and share the stop codon. Here, we studied the occurrence of this genetic arrangement in endolysins, the phage enzymes that cut the bacterial cell wall peptidoglycan to release the virion progeny. After screening over 3,000 endolysin sequences of phages infecting Gram-positive bacteria, we found evidence that this coding strategy is frequent in endolysin genes. Our bioinformatics predictions were experimentally validated by demonstrating that two polypeptides are indeed produced from these genes. Additionally, we show that in some cases the two polypeptides need to interact and multimerize to generate the active endolysin. By studying in detail one selected example, we uncovered a heteromeric endolysin with a 1:5 subunit stoichiometry that has never been described before. Hence, we conclude that the occurrence of endolysin genes encoding two polypeptide isoforms by in-frame overlapping ORFs, as well as their organization as enzymatic complexes, appears more common than previously thought, therefore challenging the established view of endolysins being mostly formed by single, monomeric polypeptide chains. IMPORTANCE Bacteriophages use endolysins to cleave the host bacteria cell wall, a crucial event underlying cell lysis for virion progeny release. These bacteriolytic enzymes are generally thought to work as single, monomeric polypeptides, but a few examples have been described in which a single gene produces two endolysin isoforms. These are encoded by two in-frame overlapping ORFs, with a shorter ORF being defined by an internal translation start site. This work shows evidence that this endolysin coding strategy is frequent in phages infecting Gram-positive bacteria, and not just an eccentricity of a few phages. In one example studied in detail, we show that the two isoforms are inactive until they assemble to generate a multimeric active endolysin, with a 1:5 subunit stoichiometry never described before. This study challenges the established view of endolysins, with possible implications in their current exploration and design as alternative antibacterials.
Collapse
Affiliation(s)
- Daniela Pinto
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Raquel Gonçalo
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Mariana Louro
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, MARE – Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Marta Sousa Silva
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, MARE – Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, MARE – Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Carlos São-José
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
43
|
Mielecki M, Ziemniak M, Ozga M, Borowski R, Antosik J, Kaczyńska A, Pająk B. Structure-Activity Relationship of the Dimeric and Oligomeric Forms of a Cytotoxic Biotherapeutic Based on Diphtheria Toxin. Biomolecules 2022; 12:biom12081111. [PMID: 36009005 PMCID: PMC9406121 DOI: 10.3390/biom12081111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Protein aggregation is a well-recognized problem in industrial preparation, including biotherapeutics. These low-energy states constantly compete with a native-like conformation, which is more pronounced in the case of macromolecules of low stability in the solution. A better understanding of the structure and function of such aggregates is generally required for the more rational development of therapeutic proteins, including single-chain fusion cytotoxins to target specific receptors on cancer cells. Here, we identified and purified such particles as side products of the renaturation process of the single-chain fusion cytotoxin, composed of two diphtheria toxin (DT) domains and interleukin 13 (IL-13), and applied various experimental techniques to comprehensively understand their molecular architecture and function. Importantly, we distinguished soluble purified dimeric and fractionated oligomeric particles from aggregates. The oligomers are polydisperse and multimodal, with a distribution favoring lower and even stoichiometries, suggesting they are composed of dimeric building units. Importantly, all these oligomeric particles and the monomer are cystine-dependent as their innate disulfide bonds have structural and functional roles. Their reduction triggers aggregation. Presumably the dimer and lower oligomers represent the metastable state, retaining the native disulfide bond. Although significantly reduced in contrast to the monomer, they preserve some fraction of bioactivity, manifested by their IL-13RA2 receptor affinity and selective cytotoxic potency towards the U-251 glioblastoma cell line. These molecular assemblies probably preserve structural integrity and native-like fold, at least to some extent. As our study demonstrated, the dimeric and oligomeric cytotoxin may be an exciting model protein, introducing a new understanding of its monomeric counterpart’s molecular characteristics.
Collapse
|
44
|
Guan X, Cheryala N, Karim RM, Chan A, Berndt N, Qi J, Georg GI, Schönbrunn E. Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity. J Med Chem 2022; 65:10441-10458. [PMID: 35867655 DOI: 10.1021/acs.jmedchem.2c00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bromodomain and extraterminal domain (BET) proteins are important regulators of gene transcription and chromatin remodeling. BET family members BRD4 and BRDT are validated targets for cancer and male contraceptive drug development, respectively. Due to the high structural similarity of the acetyl-lysine binding sites, most reported inhibitors lack intra-BET selectivity. We surmised that protein-protein interactions induced by bivalent inhibitors may differ between BRD4 and BRDT, conferring an altered selectivity profile. Starting from nonselective monovalent inhibitors, we developed cell-active bivalent BET inhibitors with increased activity and selectivity for BRDT. X-ray crystallographic and solution studies revealed unique structural states of BRDT and BRD4 upon interaction with bivalent inhibitors. Varying spacer lengths and symmetric vs unsymmetric connections resulted in the same dimeric states, whereas different chemotypes induced different dimers. The findings indicate that the increased intra-BET selectivity of bivalent inhibitors is due to the differential plasticity of BET bromodomains upon inhibitor-induced dimerization.
Collapse
Affiliation(s)
- Xianghong Guan
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Narsihmulu Cheryala
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Rezaul Md Karim
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Alice Chan
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Norbert Berndt
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States
| | - Ernst Schönbrunn
- Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| |
Collapse
|
45
|
Sharma N, Thompson MK, Arrington JF, Terry DM, Chakravarthy S, Prevelige PE, Prakash A. Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A. Front Cell Dev Biol 2022; 10:893806. [PMID: 35938152 PMCID: PMC9354671 DOI: 10.3389/fcell.2022.893806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.
Collapse
Affiliation(s)
- Nidhi Sharma
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Marlo K. Thompson
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Jennifer F. Arrington
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Dava M. Terry
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Srinivas Chakravarthy
- Advanced Photon Source, Illinois Institute of Technology, Chicago, IL, United States
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Aishwarya Prakash
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| |
Collapse
|
46
|
Bon C, Cabantous S, Julien S, Guillet V, Chalut C, Rima J, Brison Y, Malaga W, Sanchez-Dafun A, Gavalda S, Quémard A, Marcoux J, Waldo GS, Guilhot C, Mourey L. Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis. BMC Biol 2022; 20:147. [PMID: 35729566 PMCID: PMC9210659 DOI: 10.1186/s12915-022-01337-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I polyketide synthases (PKSs) are multifunctional enzymes responsible for the biosynthesis of a group of diverse natural compounds with biotechnological and pharmaceutical interest called polyketides. The diversity of polyketides is impressive despite the limited set of catalytic domains used by PKSs for biosynthesis, leading to considerable interest in deciphering their structure-function relationships, which is challenging due to high intrinsic flexibility. Among nineteen polyketide synthases encoded by the genome of Mycobacterium tuberculosis, Pks13 is the condensase required for the final condensation step of two long acyl chains in the biosynthetic pathway of mycolic acids, essential components of the cell envelope of Corynebacterineae species. It has been validated as a promising druggable target and knowledge of its structure is essential to speed up drug discovery to fight against tuberculosis. RESULTS We report here a quasi-atomic model of Pks13 obtained using small-angle X-ray scattering of the entire protein and various molecular subspecies combined with known high-resolution structures of Pks13 domains or structural homologues. As a comparison, the low-resolution structures of two other mycobacterial polyketide synthases, Mas and PpsA from Mycobacterium bovis BCG, are also presented. This study highlights a monomeric and elongated state of the enzyme with the apo- and holo-forms being identical at the resolution probed. Catalytic domains are segregated into two parts, which correspond to the condensation reaction per se and to the release of the product, a pivot for the enzyme flexibility being at the interface. The two acyl carrier protein domains are found at opposite sides of the ketosynthase domain and display distinct characteristics in terms of flexibility. CONCLUSIONS The Pks13 model reported here provides the first structural information on the molecular mechanism of this complex enzyme and opens up new perspectives to develop inhibitors that target the interactions with its enzymatic partners or between catalytic domains within Pks13 itself.
Collapse
Affiliation(s)
- Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Stéphanie Cabantous
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA
- Present address: Centre de Recherche en Cancérologie de Toulouse (CRCT), Inserm, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylviane Julien
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julie Rima
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yoann Brison
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Present address: Toulouse White Biotechnology, 31400, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Angelique Sanchez-Dafun
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Present address: Carbios, Biopole Clermont Limagne, 63360, Saint-Beauzire, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geoffrey S Waldo
- Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
| |
Collapse
|
47
|
Wickramaratne AC, Li L, Hopkins JB, Joachimiak LA, Green CB. The Disordered Amino Terminus of the Circadian Enzyme Nocturnin Modulates Its NADP(H) Phosphatase Activity by Changing Protein Dynamics. Biochemistry 2022; 61:10.1021/acs.biochem.2c00072. [PMID: 35535990 PMCID: PMC9646931 DOI: 10.1021/acs.biochem.2c00072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Endogenous circadian clocks control the rhythmicity of a broad range of behavioral and physiological processes, and this is entrained by the daily fluctuations in light and dark. Nocturnin (Noct) is a rhythmically expressed gene regulated by the circadian clock that belongs to the CCR4 family of endonuclease-exonuclease-phosphatase (EEP) enzymes, and the NOCT protein exhibits phosphatase activity, catalyzing the removal of the 2'-phosphate from NADP(H). In addition to its daily nighttime peak of expression, it is also induced by acute stimuli. Loss of Nocturnin (Noct-/-) in mice results in resistance to high-fat diet-induced obesity, and loss of Noct in HEK293T cells confers a protective effect to oxidative stress. Modeling of the full-length Nocturnin protein reveals a partially structured amino terminus that is disparate from its CCR4 family members. The high sequence conservation of a leucine zipper-like (LZ-like) motif, the only structural element in the amino terminus, highlights the potential importance of this domain in modulating phosphatase activity. In vitro biochemical and biophysical techniques demonstrate that the LZ-like domain within the flexible N-terminus is necessary for preserving the active site cleft in an optimal conformation to promote the efficient turnover of the substrate. This modulation occurs in cis and is pivotal in maintaining the stability and conformational integrity of the enzyme. These new findings suggest an additional layer of modulating the activity of Nocturnin in addition to its rhythmicity to provide fine-tuned control over cellular levels of NADPH.
Collapse
Affiliation(s)
- Anushka C. Wickramaratne
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Li Li
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jesse B. Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Lukasz A. Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carla B. Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
48
|
Cerqueira FM, Photenhauer AL, Doden HL, Brown AN, Abdel-Hamid AM, Moraïs S, Bayer EA, Wawrzak Z, Cann I, Ridlon JM, Hopkins JB, Koropatkin NM. Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome. J Biol Chem 2022; 298:101896. [PMID: 35378131 PMCID: PMC9112005 DOI: 10.1016/j.jbc.2022.101896] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure-function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.
Collapse
Affiliation(s)
- Filipe M Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Aric N Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ahmed M Abdel-Hamid
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edward A Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zdzislaw Wawrzak
- Northwestern University, Synchrotron Research Center, Life Science Collaborative Access Team, Lemont, Illinois, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| |
Collapse
|
49
|
Courbet A, Hansen J, Hsia Y, Bethel N, Park YJ, Xu C, Moyer A, Boyken S, Ueda G, Nattermann U, Nagarajan D, Silva D, Sheffler W, Quispe J, Nord A, King N, Bradley P, Veesler D, Kollman J, Baker D. Computational design of mechanically coupled axle-rotor protein assemblies. Science 2022; 376:383-390. [PMID: 35446645 PMCID: PMC10712554 DOI: 10.1126/science.abm1183] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.
Collapse
Affiliation(s)
- A. Courbet
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Hansen
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Y. Hsia
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - N. Bethel
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - YJ. Park
- Department of Biochemistry, University of Washington, Seattle, USA
| | - C. Xu
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - A. Moyer
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - S.E. Boyken
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - G. Ueda
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - U. Nattermann
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Nagarajan
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Silva
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Monod Bio, Inc, Seattle, USA
| | - W. Sheffler
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - J. Quispe
- Department of Biochemistry, University of Washington, Seattle, USA
| | - A. Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - N. King
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - P. Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - D. Veesler
- Department of Biochemistry, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Kollman
- Department of Biochemistry, University of Washington, Seattle, USA
| | - D. Baker
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| |
Collapse
|
50
|
Molodenskiy DS, Svergun DI, Kikhney AG. Artificial neural networks for solution scattering data analysis. Structure 2022; 30:900-908.e2. [DOI: 10.1016/j.str.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
|