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Bartošík V, Plucarová J, Laníková A, Janáčková Z, Padrta P, Jansen S, Vařečka V, Gruber T, Feller SM, Žídek L. Structural basis of binding the unique N-terminal domain of microtubule-associated protein 2c to proteins regulating kinases of signaling pathways. J Biol Chem 2024; 300:107551. [PMID: 39002671 DOI: 10.1016/j.jbc.2024.107551] [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: 04/23/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/15/2024] Open
Abstract
Isoforms of microtubule-associated protein 2 (MAP2) differ from their homolog Tau in the sequence and interactions of the N-terminal region. Binding of the N-terminal region of MAP2c (N-MAP2c) to the dimerization/docking domains of the regulatory subunit RIIα of cAMP-dependent protein kinase (RIIDD2) and to the Src-homology domain 2 (SH2) of growth factor receptor-bound protein 2 (Grb2) have been described long time ago. However, the structural features of the complexes remained unknown due to the disordered nature of MAP2. Here, we provide structural description of the complexes. We have solved solution structure of N-MAP2c in complex with RIIDD2, confirming formation of an amphiphilic α-helix of MAP2c upon binding, defining orientation of the α-helix in the complex and showing that its binding register differs from previous predictions. Using chemical shift mapping, we characterized the binding interface of SH2-Grb2 and rat MAP2c phosphorylated by the tyrosine kinase Fyn in their complex and proposed a model explaining differences between SH2-Grb2 complexes with rat MAP2c and phosphopeptides with a Grb2-specific sequence. The results provide the structural basis of a potential role of MAP2 in regulating cAMP-dependent phosphorylation cascade via interactions with RIIDD2 and Ras signaling pathway via interactions with SH2-Grb2.
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Affiliation(s)
- Viktor Bartošík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jitka Plucarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alice Laníková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Janáčková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Padrta
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Séverine Jansen
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtěch Vařečka
- Institute of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tobias Gruber
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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2
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Develin A, Fuglestad B. Inositol Hexaphosphate as an Inhibitor and Potential Regulator of p47 phox Membrane Anchoring. Biochemistry 2024; 63:1097-1106. [PMID: 38669178 PMCID: PMC11080064 DOI: 10.1021/acs.biochem.4c00117] [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: 03/02/2024] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
As a key component for NADPH oxidase 2 (NOX2) activation, the peripheral membrane protein p47phox translocates a cytosolic activating complex to the membrane through its PX domain. This study elucidates a potential regulatory mechanism of p47phox recruitment and NOX2 activation by inositol hexaphosphate (IP6). Through NMR, fluorescence polarization, and FRET experimental results, IP6 is shown to be capable of breaking the lipid binding and membrane anchoring events of p47phox-PX with low micromolar potency. Other phosphorylated inositol species such as IP5(1,3,4,5,6), IP4(1,3,4,5), and IP3(1,3,4) show weaker binding and no ability to inhibit lipid interactions in physiological concentration ranges. The low micromolar potency of IP6 inhibition of the p47phox membrane anchoring suggests that physiologically relevant concentrations of IP6 serve as regulators, as seen in other membrane anchoring domains. The PX domain of p47phox is known to be promiscuous to a variety of phosphatidylinositol phosphate (PIP) lipids, and this regulation may help target the domain only to the membranes most highly enriched with the highest affinity PIPs, such as the phagosomal membrane, while preventing aberrant binding to other membranes with high and heterogeneous PIP content, such as the plasma membrane. This study provides insight into a potential novel regulatory mechanism behind NOX2 activation and reveals a role for small-molecule regulation in this important NOX2 activator.
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Affiliation(s)
- Angela
M. Develin
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
| | - Brian Fuglestad
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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3
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Stadler KA, Ortiz-Joya LJ, Singh Sahrawat A, Buhlheller C, Gruber K, Pavkov-Keller T, O'Hagan TB, Guarné A, Pulido S, Marín-Villa M, Zangger K, Gubensäk N. Structural investigation of Trypanosoma cruzi Akt-like kinase as drug target against Chagas disease. Sci Rep 2024; 14:10039. [PMID: 38693166 PMCID: PMC11063076 DOI: 10.1038/s41598-024-59654-8] [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: 01/19/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
According to the World Health Organization, Chagas disease (CD) is the most prevalent poverty-promoting neglected tropical disease. Alarmingly, climate change is accelerating the geographical spreading of CD causative parasite, Trypanosoma cruzi, which additionally increases infection rates. Still, CD treatment remains challenging due to a lack of safe and efficient drugs. In this work, we analyze the viability of T. cruzi Akt-like kinase (TcAkt) as drug target against CD including primary structural and functional information about a parasitic Akt protein. Nuclear Magnetic Resonance derived information in combination with Molecular Dynamics simulations offer detailed insights into structural properties of the pleckstrin homology (PH) domain of TcAkt and its binding to phosphatidylinositol phosphate ligands (PIP). Experimental data combined with Alpha Fold proposes a model for the mechanism of action of TcAkt involving a PIP-induced disruption of the intramolecular interface between the kinase and the PH domain resulting in an open conformation enabling TcAkt kinase activity. Further docking experiments reveal that TcAkt is recognized by human inhibitors PIT-1 and capivasertib, and TcAkt inhibition by UBMC-4 and UBMC-6 is achieved via binding to TcAkt kinase domain. Our in-depth structural analysis of TcAkt reveals potential sites for drug development against CD, located at activity essential regions.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Lesly J Ortiz-Joya
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Amit Singh Sahrawat
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | | | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Sergio Pulido
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- LifeFactors ZF SAS, Rionegro, Colombia
| | - Marcel Marín-Villa
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - Nina Gubensäk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
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4
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Aljedani SS, Aldehaiman A, Sandholu A, Alharbi S, Mak VC, Wu H, Lugari A, Jaremko M, Morelli X, Backer JW, Ladbury JE, Nowakowski M, Cheung LW, Arold ST. Functional selection in SH3-mediated activation of the PI3 kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591319. [PMID: 38746413 PMCID: PMC11092569 DOI: 10.1101/2024.04.30.591319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The phosphoinositide-3 kinase (PI3K), a heterodimeric enzyme, plays a pivotal role in cellular metabolism and survival. Its deregulation is associated with major human diseases, particularly cancer. The p85 regulatory subunit of PI3K binds to the catalytic p110 subunit via its C-terminal domains, stabilising it in an inhibited state. Certain Src homology 3 (SH3) domains can activate p110 by binding to the proline-rich (PR) 1 motif located at the N-terminus of p85. However, the mechanism by which this N-terminal interaction activates the C-terminally bound p110 remains elusive. Moreover, the intrinsically poor ligand selectivity of SH3 domains raises the question of how they can control PI3K. Combining structural, biophysical, and functional methods, we demonstrate that the answers to both these unknown issues are linked: PI3K-activating SH3 domains engage in additional "tertiary" interactions with the C-terminal domains of p85, thereby relieving their inhibition of p110. SH3 domains lacking these tertiary interactions may still bind to p85 but cannot activate PI3K. Thus, p85 uses a functional selection mechanism that precludes nonspecific activation rather than nonspecific binding. This separation of binding and activation may provide a general mechanism for how biological activities can be controlled by promiscuous protein-protein interaction domains.
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Affiliation(s)
- Safia S. Aljedani
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Abdullah Aldehaiman
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Anandsukeerthi Sandholu
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Siba Alharbi
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Victor C.Y. Mak
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Haiyan Wu
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Adrien Lugari
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Xavier Morelli
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France
| | - Jonathan W. Backer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John E. Ladbury
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Lydia W.T. Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
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5
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Giudice J, Brauer DD, Zoltek M, Vázquez Maldonado AL, Kelly M, Schepartz A. Requirements for efficient endosomal escape by designed mini-proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588336. [PMID: 38617268 PMCID: PMC11014610 DOI: 10.1101/2024.04.05.588336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
ZF5.3 is a compact, rationally designed mini-protein that escapes efficiently from the endosomes of multiple cell types. Despite its small size (27 amino acids), ZF5.3 can be isolated intact from the cytosol of treated cells and guides multiple classes of proteins into the cytosol and/or nucleus. In the best cases, delivery efficiencies reach or exceed 50% to establish nuclear or cytosolic concentrations of 500 nM or higher. But other than the requirement for unfoldable cargo and an intact HOPS complex, there is little known about how ZF5.3 traverses the limiting endocytic membrane. Here we delineate the attributes of ZF5.3 that enable efficient endosomal escape. We confirm that ZF5.3 is stable at pH values between 5.5 and 7.5, with no evidence of unfolding even at temperatures as high as 95 °C. The high-resolution NMR structure of ZF5.3 at pH 5.5, also reported here, shows a canonical p zinc-finger fold with the penta-arg motif integrated seamlessly into the C-terminal α-helix. At lower pH, ZF5.3 unfolds cooperatively as judged by both circular dichroism and high-resolution NMR. Unfolding occurs upon protonation of a single Zn(II)-binding His side chain whose pKa corresponds almost exactly to that of the late endosomal lumen. pH-induced unfolding is essential for endosomal escape, as a ZF5.3 analog that remains folded at pH 4.5 fails to efficiently reach the cytosol, despite high overall uptake. Finally, using reconstituted liposomes, we identify a high-affinity interaction of ZF5.3 with a specific lipid-BMP-that is selectively enriched in the inner leaflet of late endosomal membranes. This interaction is 10-fold stronger at low pH than neutral pH, providing a molecular picture for why escape occurs preferentially and in a HOPS-dependent manner from late endosomal compartments. The requirements for programmed endosomal escape identified here should aid and inform the design of proteins, peptidomimetics, and other macromolecules that reach cytosolic or nuclear targets intact and at therapeutically relevant concentrations.
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Affiliation(s)
- Jonathan Giudice
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Daniel D. Brauer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Madeline Zoltek
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720
| | | | - Mark Kelly
- School of Pharmacy, University of California-San Francisco, San Francisco, CA 94158
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Arc Institute, Palo Alto, CA
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6
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Wang Q, DiForte C, Aleshintsev A, Elci G, Bhattacharya S, Bongiorno A, Gupta R. Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins. Protein Sci 2024; 33:e4955. [PMID: 38501487 PMCID: PMC10949321 DOI: 10.1002/pro.4955] [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: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein. Elimination of binding in S100-specific EF-I loop has limited impact on the calcium binding affinity of the EF-II loop and the concomitant structural rearrangement. In contrast, deletion of binding in the EF-II loop significantly attenuates calcium affinity in the EF-I loop and the structure adopts a 'closed' apo-like conformation. Analysis of experimental amide nitrogen (15 N) relaxation rates (R1 , R2 , and 15 N-{1 H} NOE) and molecular dynamics (MD) simulations demonstrate that the calcium bound state is relatively floppy with pico-nanosecond motions induced in functionally relevant domains responsible for target recognition such as the hinge domain and the C-terminal residues. Experimental relaxation studies combined with MD simulations show that while calcium binding in the EF-I loop alone does not induce significant motions in the polypeptide chain, EF-I regulates fluctuations in the polypeptide in the presence of bound calcium in the EF-II loop. These results offer novel insights into the dynamic regulation of target recognition by calcium binding and unravels the role of cooperativity between the two calcium binding events in S100A12.
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Affiliation(s)
- Qian Wang
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | - Christopher DiForte
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Aleksey Aleshintsev
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Gianna Elci
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | | | - Angelo Bongiorno
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Rupal Gupta
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
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7
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Lee H, Park SH, Kim J, Lee J, Koh MS, Lee JH, Kim S. Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305946. [PMID: 37987032 PMCID: PMC10787088 DOI: 10.1002/advs.202305946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiyoon Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehak Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min Sun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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8
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McKenna S, Aylward F, Miliara X, Lau RJ, Huemer CB, Giblin SP, Huse KK, Liang M, Reeves L, Pearson M, Xu Y, Rouse SL, Pease JE, Sriskandan S, Kagawa TF, Cooney J, Matthews S. The protease associated (PA) domain in ScpA from Streptococcus pyogenes plays a role in substrate recruitment. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140946. [PMID: 37562488 DOI: 10.1016/j.bbapap.2023.140946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Annually, over 18 million disease cases and half a million deaths worldwide are estimated to be caused by Group A Streptococcus. ScpA (or C5a peptidase) is a well characterised member of the cell enveleope protease family, which possess a S8 subtilisin-like catalytic domain and a shared multi-domain architecture. ScpA cleaves complement factors C5a and C3a, impairing the function of these critical anaphylatoxins and disrupts complement-mediated innate immunity. Although the high resolution structure of ScpA is known, the details of how it recognises its substrate are only just emerging. Previous studies have identified a distant exosite on the 2nd fibronectin domain that plays an important role in recruitment via an interaction with the substrate core. Here, using a combination of solution NMR spectroscopy, mutagenesis with functional assays and computational approaches we identify a second exosite within the protease-associated (PA) domain. We propose a model in which the PA domain assists optimal delivery of the substrate's C terminus to the active site for cleavage.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Frances Aylward
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Rikin J Lau
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Camilla Berg Huemer
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sean P Giblin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Mingyang Liang
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Lucy Reeves
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - James E Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Todd F Kagawa
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Jakki Cooney
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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9
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Kolonko-Adamska M, Zawadzka-Kazimierczuk A, Bartosińska-Marzec P, Koźmiński W, Popowicz G, Krężel A, Ożyhar A, Greb-Markiewicz B. Interaction patterns of methoprene-tolerant and germ cell-expressed Drosophila JH receptors suggest significant differences in their functioning. Front Mol Biosci 2023; 10:1215550. [PMID: 37654797 PMCID: PMC10465699 DOI: 10.3389/fmolb.2023.1215550] [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: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Methoprene-tolerant (Met) and germ cell-expressed (Gce) proteins were shown to be juvenile hormone (JH) receptors of Drosophila melanogaster with partially redundant functions. We raised the question of where the functional differentiation of paralogs comes from. Therefore, we tested Met and Gce interaction patterns with selected partners. In this study, we showed the ability of Gce and its C-terminus (GceC) to interact with 14-3-3 in the absence of JH. In contrast, Met or Met C-terminus (MetC) interactions with 14-3-3 were not observed. We also performed a detailed structural analysis of Met/Gce interactions with the nuclear receptor fushi tarazu factor-1 (Ftz-F1) ligand-binding domain. We showed that GceC comprising an Ftz-F1-binding site and full-length protein interacts with Ftz-F1. In contrast to Gce, only MetC (not full-length Met) can interact with Ftz-F1 in the absence of JH. We propose that the described differences result from the distinct tertiary structure and accessibility of binding sites in the full-length Met/Gce. Moreover, we hypothesize that each interacting partner can force disordered MetC and GceC to change the structure in a partner-specific manner. The observed interactions seem to determine the subcellular localization of Met/Gce by forcing their translocation between the nucleus and the cytoplasm, which may affect the activity of the proteins. The presented differences between Met and Gce can be crucial for their functional differentiation during D. melanogaster development and indicate Gce as a more universal and more active paralog. It is consistent with the theory indicating gce as an ancestor gene.
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Affiliation(s)
- M. Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - A. Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - P. Bartosińska-Marzec
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - W. Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - G. Popowicz
- Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - A. Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - A. Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - B. Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
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10
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Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J. FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 2023:S1097-2765(23)00516-6. [PMID: 37506698 DOI: 10.1016/j.molcel.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
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Affiliation(s)
| | - Clara Hipp
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany
| | | | | | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Cem Bakisoglu
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kerstin Tretow
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; CardioPulmonary Institute (CPI), 35392 Gießen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Center (S-BIK-F), 60325 Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt am Main, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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11
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Chaves-Arquero B, Collins KM, Abis G, Kelly G, Christodoulou E, Taylor IA, Ramos A. Affinity-enhanced RNA-binding domains as tools to understand RNA recognition. CELL REPORTS METHODS 2023; 3:100508. [PMID: 37426752 PMCID: PMC10326445 DOI: 10.1016/j.crmeth.2023.100508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/14/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023]
Abstract
Understanding how the RNA-binding domains of a protein regulator are used to recognize its RNA targets is a key problem in RNA biology, but RNA-binding domains with very low affinity do not perform well in the methods currently available to characterize protein-RNA interactions. Here, we propose to use conservative mutations that enhance the affinity of RNA-binding domains to overcome this limitation. As a proof of principle, we have designed and validated an affinity-enhanced K-homology (KH) domain mutant of the fragile X syndrome protein FMRP, a key regulator of neuronal development, and used this mutant to determine the domain's sequence preference and to explain FMRP recognition of specific RNA motifs in the cell. Our results validate our concept and our nuclear magnetic resonance (NMR)-based workflow. While effective mutant design requires an understanding of the underlying principles of RNA recognition by the relevant domain type, we expect the method will be used effectively in many RNA-binding domains.
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Affiliation(s)
- Belén Chaves-Arquero
- Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6AA, UK
- Department of Structural and Chemical Biology, Center for Biological Research, CIB, CSIC, Av. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Katherine M. Collins
- Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6AA, UK
| | - Giancarlo Abis
- Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6AA, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6AA, UK
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12
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Petersen M, Fang R, Majumdar A, Barrick D. Stability Islands and the Folding Cooperativity of a Seven-Repeat Array from Topoisomerase V. J Am Chem Soc 2023; 145:12641-12650. [PMID: 37262333 PMCID: PMC10416711 DOI: 10.1021/jacs.3c02193] [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] [Indexed: 06/03/2023]
Abstract
Cooperativity is a central feature of protein folding, but the thermodynamic and structural origins of cooperativity remain poorly understood. To quantify cooperativity, we measured guanidine-induced unfolding transitions of single helix-hairpin-helix (HhH)2 repeats and tandem pairs from a seven-repeat segment of Methanopyrus kandleri Topoisomerase V (Topo V) to determine intrinsic repeat stability and interfacial free energies between repeats. Most single-repeat constructs are folded and stable; moreover, several pairs have unfolding midpoints that exceed midpoints of the single repeats they comprise, demonstrating favorable coupling between repeats. Analyzing unfolding transitions with a modified Ising model, we find a broad range of intrinsic and interfacial free energies. Surprisingly, the G repeat, which lacks density in the crystal structure of Topo V without DNA, is the most stable repeat in the array. Using nuclear magnetic resonance spectroscopy, we demonstrate that the isolated G repeat adopts a canonical (HhH)2 fold and forms an ordered interface with the F-repeat but not with the H repeat. Using parameters from our paired Ising fit, we built a partition function for the seven-repeat array. The multistate unfolding transition predicted from this partition function is in excellent agreement with the experimental unfolding transition, providing strong justification for the nearest-neighbor model. The seven-repeat partition function predicts a native state in which three independent segments ("stability islands") of interacting repeats are separated by two unstable interfaces. We confirm this segmented architecture by measuring the unfolding transition of an equimolar mixture of these three separate polypeptides. This segmented structural organization may facilitate wrapping around DNA.
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Affiliation(s)
- Mark Petersen
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Rebecca Fang
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, Johns Hopkins University
| | - Doug Barrick
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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13
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Chen JCH, Tonelli M, Anderson P, Michalczyk R, Blum MM, Williams RF. Backbone and side chain chemical shift assignment of diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris, an organophosphorus-degrading enzyme. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:55-60. [PMID: 36763236 DOI: 10.1007/s12104-023-10120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/24/2023] [Indexed: 06/02/2023]
Abstract
NMR chemical shift assignments are reported for backbone (15N, 1H) and partial side chain (13Cα and β, side chain 1H) atoms of diisopropyl fluorophosphatase (DFPase), a calcium-dependent phosphotriesterase capable of hydrolyzing phosphorus - fluorine bonds in a variety of toxic organophosphorus compounds. Analysis of residues lining the active site of DFPase highlight a number of residues whose chemical shifts can be used as a diagnostic of binding and detection of organophosphorus compounds.
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Affiliation(s)
- Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA.
| | - Marco Tonelli
- Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, 433 Babcock Drive, 53706-1544, Madison, WI, USA
| | - Penelope Anderson
- Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
| | - Ryszard Michalczyk
- Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
| | - Marc-Michael Blum
- Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
- Blum Scientific Services, Hamburg, Germany
| | - Robert F Williams
- Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA
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14
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Rennella E, Sahtoe DD, Baker D, Kay LE. Exploiting conformational dynamics to modulate the function of designed proteins. Proc Natl Acad Sci U S A 2023; 120:e2303149120. [PMID: 37094170 PMCID: PMC10161014 DOI: 10.1073/pnas.2303149120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics is encoded by the primary protein sequence so as to better predict function. Such dynamics information is critical for protein design, where strategies could then focus not only on sequences that fold into particular structures that perform a given task, but would also include low-lying excited protein states that could influence the function of the designed protein. Herein, we illustrate the importance of dynamics in modulating the function of C34, a designed α/β protein that captures β-strands of target ligands and is a member of a family of proteins designed to sequester β-strands and β hairpins of aggregation-prone molecules that lead to a variety of pathologies. Using a strategy to "see" regions of apo C34 that are invisible to NMR spectroscopy as a result of pervasive conformational exchange, as well as a mutagenesis approach whereby C34 molecules are stabilized into a single conformer, we determine the structures of the predominant conformations that are sampled by C34 and show that these attenuate the affinity for cognate peptide. Subsequently, the observed motion is exploited to develop an allosterically regulated peptide binder whose binding affinity can be controlled through the addition of a second molecule. Our study emphasizes the unique role that NMR can play in directing the design process and in the construction of new molecules with more complex functionality.
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Affiliation(s)
- Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, ONM5S 3H6, Canada
| | - Danny D. Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
| | - Lewis E. Kay
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, ONM5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ONM5G 0A4, Canada
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15
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Verma D, Hegde V, Kirkpatrick J, Carlomagno T. The EJC disassembly factor PYM is an intrinsically disordered protein and forms a fuzzy complex with RNA. Front Mol Biosci 2023; 10:1148653. [PMID: 37065448 PMCID: PMC10098021 DOI: 10.3389/fmolb.2023.1148653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
The discovery of several functional interactions where one or even both partners remain disordered has demonstrated that specific interactions do not necessarily require well-defined intermolecular interfaces. Here we describe a fuzzy protein–RNA complex formed by the intrinsically unfolded protein PYM and RNA. PYM is a cytosolic protein, which has been reported to bind the exon junction complex (EJC). In the process of oskar mRNA localization in Drosophila melanogaster, removal of the first intron and deposition of the EJC are essential, while PYM is required to recycle the EJC components after localization has been accomplished. Here we demonstrate that the first 160 amino acids of PYM (PYM1–160) are intrinsically disordered. PYM1–160 binds RNA independently of its nucleotide sequence, forming a fuzzy protein–RNA complex that is incompatible with PYM’s function as an EJC recycling factor. We propose that the role of RNA binding consists in down-regulating PYM activity by blocking the EJC interaction surface of PYM until localization has been accomplished. We suggest that the largely unstructured character of PYM may act to enable binding to a variety of diverse interaction partners, such as multiple RNA sequences and the EJC proteins Y14 and Mago.
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Affiliation(s)
- Deepshikha Verma
- Laboratory of NMR-based Integrative Structural Biology, Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Hanover, Germany
| | - Veena Hegde
- Laboratory of NMR-based Integrative Structural Biology, Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Hanover, Germany
| | - John Kirkpatrick
- Laboratory of Integrative Structural Biology, School of Biosciences, College of LES, University of Birmingham, Birmingham, United Kingdom
| | - Teresa Carlomagno
- Laboratory of Integrative Structural Biology, School of Biosciences, College of LES, University of Birmingham, Birmingham, United Kingdom
- *Correspondence: Teresa Carlomagno,
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16
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Bishop AC, Torres-Montalvo G, Kotaru S, Mimun K, Wand AJ. Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing. Nat Commun 2023; 14:1556. [PMID: 36944645 PMCID: PMC10030768 DOI: 10.1038/s41467-023-37219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Assignment of resonances of nuclear magnetic resonance (NMR) spectra to specific atoms within a protein remains a labor-intensive and challenging task. Automation of the assignment process often remains a bottleneck in the exploitation of solution NMR spectroscopy for the study of protein structure-dynamics-function relationships. We present an approach to the assignment of backbone triple resonance spectra of proteins. A Bayesian statistical analysis of predicted and observed chemical shifts is used in conjunction with inter-spin connectivities provided by triple resonance spectroscopy to calculate a pseudo-energy potential that drives a simulated annealing search for the most optimal set of resonance assignments. Termed Bayesian Assisted Assignments by Simulated Annealing (BARASA), a C++ program implementation is tested against systems ranging in size to over 450 amino acids including examples of intrinsically disordered proteins. BARASA is fast, robust, accommodates incomplete and incorrect information, and outperforms current algorithms - especially in cases of sparse data and is sufficiently fast to allow for real-time evaluation during data acquisition.
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Affiliation(s)
- Anthony C Bishop
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Glorisé Torres-Montalvo
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Sravya Kotaru
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19014, USA
| | - Kyle Mimun
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19014, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
- Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA.
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17
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Kwon Y, Rösner H, Zhao W, Selemenakis P, He Z, Kawale AS, Katz JN, Rogers CM, Neal FE, Badamchi Shabestari A, Petrosius V, Singh AK, Joel MZ, Lu L, Holloway SP, Burma S, Mukherjee B, Hromas R, Mazin A, Wiese C, Sørensen CS, Sung P. DNA binding and RAD51 engagement by the BRCA2 C-terminus orchestrate DNA repair and replication fork preservation. Nat Commun 2023; 14:432. [PMID: 36702902 PMCID: PMC9879961 DOI: 10.1038/s41467-023-36211-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
The tumor suppressor BRCA2 participates in DNA double-strand break repair by RAD51-dependent homologous recombination and protects stressed DNA replication forks from nucleolytic attack. We demonstrate that the C-terminal Recombinase Binding (CTRB) region of BRCA2, encoded by gene exon 27, harbors a DNA binding activity. CTRB alone stimulates the DNA strand exchange activity of RAD51 and permits the utilization of RPA-coated ssDNA by RAD51 for strand exchange. Moreover, CTRB functionally synergizes with the Oligonucleotide Binding fold containing DNA binding domain and BRC4 repeat of BRCA2 in RPA-RAD51 exchange on ssDNA. Importantly, we show that the DNA binding and RAD51 interaction attributes of the CTRB are crucial for homologous recombination and protection of replication forks against MRE11-mediated attrition. Our findings shed light on the role of the CTRB region in genome repair, reveal remarkable functional plasticity of BRCA2, and help explain why deletion of Brca2 exon 27 impacts upon embryonic lethality.
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Affiliation(s)
- Youngho Kwon
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Heike Rösner
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Platon Selemenakis
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhuoling He
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jeffrey N Katz
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Cody M Rogers
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Francisco E Neal
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Aida Badamchi Shabestari
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Valdemaras Petrosius
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark
| | - Akhilesh K Singh
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
- GentiBio Inc., 150 Cambridgepark Dr, Cambridge, MA, 02140, USA
| | - Marina Z Joel
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Bipasha Mukherjee
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Alexander Mazin
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark.
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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18
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Zerio CJ, Sivinski J, Wijeratne EMK, Xu YM, Ngo DT, Ambrose AJ, Villa-Celis L, Ghadirian N, Clarkson MW, Zhang DD, Horton NC, Gunatilaka AAL, Fromme R, Chapman E. Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem 2023; 66:913-933. [PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.
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Affiliation(s)
- Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - E M Kithsiri Wijeratne
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Ya-Ming Xu
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Duc T Ngo
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Luis Villa-Celis
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85719, United States
| | - Donna D Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - A A Leslie Gunatilaka
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Raimund Fromme
- School of Molecular Sciences, Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, Arizona 85287, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
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19
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Wernersson S, Bobby R, Flavell L, Milbradt AG, Holdgate GA, Embrey KJ, Akke M. Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility. Biochemistry 2022; 61:2303-2318. [PMID: 36215732 PMCID: PMC9631989 DOI: 10.1021/acs.biochem.2c00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The bromodomain and extra-terminal (BET) protein BRD4
regulates
gene expression via recruitment of transcriptional regulatory complexes
to acetylated chromatin. Like other BET proteins, BRD4 contains two
bromodomains, BD1 and BD2, that can interact cooperatively with target
proteins and designed ligands, with important implications for drug
discovery. Here, we used nuclear magnetic resonance (NMR) spectroscopy
to study the dynamics and interactions of the isolated bromodomains,
as well as the tandem construct including both domains and the intervening
linker, and investigated the effects of binding a tetra-acetylated
peptide corresponding to the tail of histone 4. The peptide affinity
is lower for both domains in the tandem construct than for the isolated
domains. Using 15N spin relaxation, we determined the global
rotational correlation times and residue-specific order parameters
for BD1 and BD2. Isolated BD1 is monomeric in the apo state but apparently
dimerizes upon binding the tetra-acetylated peptide. Isolated BD2
partially dimerizes in both the apo and peptide-bound states. The
backbone order parameters reveal marked differences between BD1 and
BD2, primarily in the acetyl-lysine binding site where the ZA loop
is more flexible in BD2. Peptide binding reduces the order parameters
of the ZA loop in BD1 and the ZA and BC loops in BD2. The AB loop,
located distally from the binding site, shows variable dynamics that
reflect the different dimerization propensities of the domains. These
results provide a basis for understanding target recognition by BRD4.
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Affiliation(s)
- Sven Wernersson
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Romel Bobby
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Liz Flavell
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, CambridgeCB4 0WG, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Geoffrey A Holdgate
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, CambridgeCB4 0WG, U.K
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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20
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Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F. Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:237-246. [PMID: 35474152 PMCID: PMC9510119 DOI: 10.1007/s12104-022-10086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein.
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Affiliation(s)
- Christoph Wiedemann
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Biostructural Interactions, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
| | - Kingsley Benjamin Obika
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Sandra Liebscher
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Jirschitzka
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Frank Bordusa
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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21
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Smith CE, Jones DNM. NMR resonance assignment of the N-terminal GTPase domain of human Miro2 Bound to GTP. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:349-355. [PMID: 36050579 PMCID: PMC9510121 DOI: 10.1007/s12104-022-10103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/23/2022] [Indexed: 05/21/2023]
Abstract
Miro2 and Miro1 are mitochondrial-associated proteins critical for regulating mitochondrial movement within the cell. Both Miro1 and Miro2 have roles in promoting neuron function, but recently Miro2 has been shown to have additional roles in response to nutrient starvation in tumor cells. Miro1 and 2 consist of two small GTPase domains flanking a pair of EF-hands. The N-terminal GTPase (nGTPase) domain is responsible for initiating mitochondrial trafficking and interactions with GCN1 in prostate cancer. The crystal structure of Miro1 nGTPase bound to GTP has been solved. However, no structural data is available for the nGTPase domain of Miro2. To better understand the similarities and differences in the functions of Miro1 and Miro2, we have initiated structural studies of Miro2. Here we report the backbone NMR chemical shift assignments of a 22 KDa construct of the nGTPase domain of Miro2 bound to GTP that includes residues 1-180 of the full-length protein. We affirm that the overall secondary structure of this complex closely resembles that of Miro1 nGTPase bound to GTP. Minor variations in the overall structures can be attributed to crystal packing interactions in the structure of Miro1. These NMR studies will form the foundation for future work identifying the specific interaction sites between Miro2 and its cellular binding partners.
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Affiliation(s)
- Cassandra E Smith
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David N M Jones
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA.
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22
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Walker K, Waters LC, Kelly G, Muskett FW, Carr MD. Sequence-specific 1H, 13C and 15N backbone NMR assignments for the N-terminal IgV-like domain (D1) and full extracellular region (D1D2) of PD-L1. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:281-288. [PMID: 35675028 PMCID: PMC9510113 DOI: 10.1007/s12104-022-10092-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 05/17/2023]
Abstract
The co-inhibitory immune checkpoint interaction between programmed cell death-protein 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) serves to regulate T-cell activation, promoting self-tolerance. Over-expression of PD-L1 is a mechanism through which tumour cells can evade detection by the immune system. Several therapeutic antibodies targeting PD-L1 or PD-1 have been approved for the treatment of a variety of cancers, however, the discovery and development of small-molecule inhibitors of PD-L1 remains a challenge. Here we report comprehensive sequence-specific backbone resonance assignments (1H, 13C, and 15N) obtained for the N-terminal IgV-like domain of PD-L1 (D1) and the full two domain extracellular region (D1D2). These NMR assignments will serve as a useful tool in the discovery of small-molecule therapeutics targeting PD-L1 and in the characterisation of functional interactions with other protein partners, such as CD80.
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Affiliation(s)
- Kayleigh Walker
- Leicester Institute of Structural and Chemical Biology, Leicester, UK.
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK.
| | - Lorna C Waters
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
| | - Geoff Kelly
- Medical Research Council (MRC) Biomedical NMR Centre, The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
| | - Frederick W Muskett
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology, Leicester, UK
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7HB, UK
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23
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Tarasca MV, Naser D, Schaefer A, Soule TG, Meiering EM. Quenched hydrogen-deuterium amide exchange optimization for high-resolution structural analysis of cellular protein aggregates. Anal Biochem 2022; 652:114675. [PMID: 35390328 DOI: 10.1016/j.ab.2022.114675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
Inclusion bodies (IBs) are large, insoluble aggregates that often form during the overexpression of proteins in bacteria. These aggregates are of broad fundamental and practical significance, for recombinant protein preparation and due to their relevance to aggregation-related medical conditions and their recent emergence as promising functional nanomaterials. Despite their significance, high resolution knowledge of IB structure remains very limited. Such knowledge will advance understanding and control of IB formation and properties in myriad practical applications. Here, we report a detailed quenched hydrogen-deuterium amide exchange (qHDX) method with NMR readout to define the structure of IBs at the level of individual residues throughout the protein. Applying proper control of experimental conditions, such as sample pH, water content, temperature, and intrinsic rate of amide exchange, yields in depth results for these cellular protein aggregates. qHDX results illustrated for Cu, Zn superoxide dismutase 1 (SOD1) and Adnectins show their IBs include native-like structure and some but not all mutations alter IB structure.
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Affiliation(s)
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Tyler Gb Soule
- Department of Chemistry, University of Waterloo, Waterloo, Canada
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24
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Specific phosphorylation of microtubule-associated protein 2c by extracellular signal-regulated kinase reduces interactions at its Pro-rich regions. J Biol Chem 2022; 298:102384. [PMID: 35987383 PMCID: PMC9520037 DOI: 10.1016/j.jbc.2022.102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022] Open
Abstract
Microtubule-associated protein 2 (MAP2) is an important neuronal target of extracellular signal-regulated kinase 2 (ERK2) involved in Raf signaling pathways, but mechanistic details of MAP2 phosphorylation are unclear. Here, we used NMR spectroscopy to quantitatively describe the kinetics of phosphorylation of individual serines and threonines in the embryonic MAP2 variant MAP2c. We carried out real-time monitoring of phosphorylation to discover major phosphorylation sites that were not identified in previous studies relying on specific antibodies. Our comparison with phosphorylation of MAP2c by a model cyclin-dependent kinase CDK2 and with phosphorylation of the MAP2c homolog Tau revealed differences in phosphorylation profiles that explain specificity of regulation of biological functions of MAP2c and Tau. To probe the molecular basis of the regulatory effect of ERK2, we investigated the interactions of phosphorylated and unphosphorylated MAP2c by NMR with single-residue resolution. As ERK2 phosphorylates mostly outside the regions binding microtubules, we studied the binding of proteins other than tubulin, namely regulatory subunit RIIα of cAMP-dependent protein kinase (PKA), adaptor protein Grb2, Src homology domain 3 of tyrosine kinases Fyn and Abl, and ERK2 itself. We found ERK2 phosphorylation interfered mostly with binding to proline-rich regions of MAP2c. Furthermore, our NMR experiments in SH-SY5Y neuroblastoma cell lysates showed that the kinetics of dephosphorylation are compatible with in-cell NMR studies and that residues targeted by ERK2 and PKA are efficiently phosphorylated in the cell lysates. Taken together, our results provide a deeper characterization of MAP2c phosphorylation and its effects on interactions with other proteins.
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25
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Yu M, Jia Y, Ma Z, Ji D, Wang C, Liang Y, Zhang Q, Yi H, Zeng L. Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer. Front Oncol 2022; 12:906807. [PMID: 36033518 PMCID: PMC9399681 DOI: 10.3389/fonc.2022.906807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
ASH1L is a member of the Trithorax-group protein and acts as a histone methyltransferase for gene transcription activation. It is known that ASH1L modulates H3K4me3 and H3K36me2/3 at its gene targets, but its specific mechanism of histone recognition is insufficiently understood. In this study, we found that the ASH1L plant homeodomain (PHD) finger interacts with mono-, di-, and trimethylated states of H3K4 peptides with comparable affinities, indicating that ASH1L PHD non-selectively binds to all three methylation states of H3K4. We solved nuclear magnetic resonance structures picturing the ASH1L PHD finger binding to the dimethylated H3K4 peptide and found that a narrow binding groove and residue composition in the methylated-lysine binding pocket restricts the necessary interaction with the dimethyl-ammonium moiety of K4. In addition, we found that the ASH1L protein is overexpressed in castrate-resistant prostate cancer (PCa) PC3 and DU145 cells in comparison to PCa LNCaP cells. The knockdown of ASH1L modulated gene expression and cellular pathways involved in apoptosis and cell cycle regulation and consequently induced cell cycle arrest, cell apoptosis, and reduced colony-forming abilities in PC3 and DU145 cells. The overexpression of the C-terminal core of ASH1L but not the PHD deletion mutant increased the overall H3K36me2 level but had no effect on the H3K4me2/3 level. Overall, our study identifies the ASH1L PHD finger as the first native reader that non-selectively recognizes the three methylation states of H3K4. Additionally, ASH1L is required for the deregulation of cell cycle and survival in PCas.
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Affiliation(s)
- Miaomiao Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Yanjie Jia
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital, Jilin University, Changchun, China
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, China
| | - Yingying Liang
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital, Jilin University, Changchun, China
- *Correspondence: Huanfa Yi, ; Lei Zeng,
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
- *Correspondence: Huanfa Yi, ; Lei Zeng,
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26
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Morando MA, Venturella F, Sollazzo M, Monaca E, Sabbatella R, Vetri V, Passantino R, Pastore A, Alfano C. Solution structure of recombinant Pvfp-5β reveals insights into mussel adhesion. Commun Biol 2022; 5:739. [PMID: 35879391 PMCID: PMC9314366 DOI: 10.1038/s42003-022-03699-w] [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: 02/02/2022] [Accepted: 07/11/2022] [Indexed: 11/27/2022] Open
Abstract
Some marine organisms can resist to aqueous tidal environments and adhere tightly on wet surface. This behavior has raised increasing attention for potential applications in medicine, biomaterials, and tissue engineering. In mussels, adhesive forces to the rock are the resultant of proteinic fibrous formations called byssus. We present the solution structure of Pvfp-5β, one of the three byssal plaque proteins secreted by the Asian green mussel Perna viridis, and the component responsible for initiating interactions with the substrate. We demonstrate that Pvfp-5β has a stably folded structure in agreement with the presence in the sequence of two EGF motifs. The structure is highly rigid except for a few residues affected by slow local motions in the µs-ms time scale, and differs from the model calculated by artificial intelligence methods for the relative orientation of the EGF modules, which is something where computational methods still underperform. We also show that Pvfp-5β is able to coacervate even with no DOPA modification, giving thus insights both for understanding the adhesion mechanism of adhesive mussel proteins, and developing of biomaterials.
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Affiliation(s)
- Maria Agnese Morando
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy
| | - Francesca Venturella
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy
| | - Martina Sollazzo
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy
| | - Raffaele Sabbatella
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy
| | - Valeria Vetri
- Department of Physics and Chemistry-Emilio Segrè (DiFC), University of Palermo, 90128, Palermo, Italy
| | - Rosa Passantino
- Biophysics Institute, National Research Council, 90143, Palermo, Italy
| | - Annalisa Pastore
- European Synchrotron Radiation Facility, Ave des Martyrs, 38000, Grenoble, France
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy.
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27
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Brown JB, Lee MA, Smith AT. The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain. J Biol Inorg Chem 2022; 27:485-495. [PMID: 35796835 PMCID: PMC9398973 DOI: 10.1007/s00775-022-01945-4] [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: 02/28/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
Most pathogenic bacteria require ferrous iron (Fe2+) in order to sustain infection within hosts. The ferrous iron transport (Feo) system is the most highly conserved prokaryotic transporter of Fe2+, but its mechanism remains to be fully characterized. Most Feo systems are composed of two proteins: FeoA, a soluble SH3-like accessory protein, and FeoB, a membrane protein that translocates Fe2+ across a lipid bilayer. Some bacterial feo operons encode FeoC, a third soluble, winged-helix protein that remains enigmatic in function. We previously demonstrated that selected FeoC proteins bind O2-sensitive [4Fe-4S] clusters via Cys residues, leading to the proposal that some FeoCs could sense O2 to regulate Fe2+ transport. However, not all FeoCs conserve these Cys residues, and FeoC from the causative agent of cholera (Vibrio cholerae) notably lacks any Cys residues, precluding cluster binding. In this work, we determined the NMR structure of VcFeoC, which is monomeric and conserves the helix-turn-helix domain seen in other FeoCs. In contrast, however, the structure of VcFeoC reveals a truncated winged β-sheet in which the cluster-binding domain is notably absent. Using homology modeling, we predicted the structure of VcNFeoB and used docking to identify an interaction site with VcFeoC, which is confirmed by NMR spectroscopy. These findings provide the first atomic-level structure of VcFeoC and contribute to a better understanding of its role vis-à-vis FeoB.
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Affiliation(s)
- Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Mark A Lee
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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28
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Sun S, Feng L, Chung KP, Lee KM, Cheung HHY, Luo M, Ren K, Law KC, Jiang L, Wong KB, Zhuang X. Mechanistic insights into an atypical interaction between ATG8 and SH3P2 in Arabidopsis thaliana. Autophagy 2022; 18:1350-1366. [PMID: 34657568 PMCID: PMC9225624 DOI: 10.1080/15548627.2021.1976965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In selective macroautophagy/autophagy, cargo receptors are recruited to the forming autophagosome by interacting with Atg8 (autophagy-related 8)-family proteins and facilitate the selective sequestration of specific cargoes for autophagic degradation. In addition, Atg8 interacts with a number of adaptors essential for autophagosome biogenesis, including ATG and non-ATG proteins. The majority of these adaptors and receptors are characterized by an Atg8-family interacting motif (AIM) for binding to Atg8. However, the molecular basis for the interaction mode between ATG8 and regulators or cargo receptors in plants remains largely unclear. In this study, we unveiled an atypical interaction mode for Arabidopsis ATG8f with a plant unique adaptor protein, SH3P2 (SH3 domain-containing protein 2), but not with the other two SH3 proteins. By structure analysis of the unbound form of ATG8f, we identified the unique conformational changes in ATG8f upon binding to the AIM sequence of a plant known autophagic receptor, NBR1. To compare the binding affinity of SH3P2-ATG8f with that of ATG8f-NBR1, we performed a gel filtration assay to show that ubiquitin-associated domain of NBR1 outcompetes the SH3 domain of SH3P2 for ATG8f interaction. Biochemical and cellular analysis revealed that distinct interfaces were employed by ATG8f to interact with NBR1 and SH3P2. Further subcellular analysis showed that the AIM-like motif of SH3P2 is essential for its recruitment to the phagophore membrane but is dispensable for its trafficking in endocytosis. Taken together, our study provides an insightful structural basis for the ATG8 binding specificity toward a plant-specific autophagic adaptor and a conserved autophagic receptor.Abbreviations: ATG, autophagy-related; AIM, Atg8-family interacting motif; BAR, Bin-Amphiphysin-Rvs; BFA, brefeldin A; BTH, benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester; CCV, clathrin-coated-vesicle; CLC2, clathrin light chain 2; Conc A, concanamycin A; ER, endoplasmic reticulum; LDS, LIR docking site; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; LIR, LC3-interacting region; PE, phosphatidylethanolamine; SH3P2, SH3 domain containing protein 2; SH3, Src-Homology-3; UBA, ubiquitin-associated; UIM, ubiquitin-interacting motif.
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Affiliation(s)
- Shuangli Sun
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanlan Feng
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Pan Chung
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ka-Ming Lee
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hayley Hei-Yin Cheung
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mengqian Luo
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kaike Ren
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Ching Law
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,CONTACT Xiaohong Zhuang Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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29
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Yang L, Lee KM, Yu CWH, Imai H, Choi AH, Banfield D, Ito K, Uchiumi T, Wong KB. The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation. Nucleic Acids Res 2022; 50:5335-5348. [PMID: 35544198 PMCID: PMC9122527 DOI: 10.1093/nar/gkac292] [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: 09/10/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic uL11 contains a conserved MPPKFDP motif at the N-terminus that is not found in archaeal and bacterial homologs. Here, we determined the solution structure of human uL11 by NMR spectroscopy and characterized its backbone dynamics by 15N-1H relaxation experiments. We showed that these N-terminal residues are unstructured and flexible. Structural comparison with ribosome-bound uL11 suggests that the linker region between the N-terminal domain and C-terminal domain of human uL11 is intrinsically disordered and only becomes structured when bound to the ribosomes. Mutagenesis studies show that the N-terminal conserved MPPKFDP motif is involved in interacting with the P-complex and its extended protuberant domain of uL10 in vitro. Truncation of the MPPKFDP motif also reduced the poly-phenylalanine synthesis in both hybrid ribosome and yeast mutagenesis studies. In addition, G→A/P substitutions to the conserved GPLG motif of helix-1 reduced poly-phenylalanine synthesis to 9-32% in yeast ribosomes. We propose that the flexible N-terminal residues of uL11, which could extend up to ∼25 Å from the N-terminal domain of uL11, can form transient interactions with the uL10 that help to fetch and fix it into a position ready for recruiting the incoming translation factors and facilitate protein synthesis.
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Affiliation(s)
- Lei Yang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ka-Ming Lee
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Conny Wing-Heng Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hirotatsu Imai
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Andrew Kwok-Ho Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - David K Banfield
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
- The Institute of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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30
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Bravo-Ferreira JFS, Cowburn D, Khoo Y, Singer A. NMR Assignment through Linear Programming. JOURNAL OF GLOBAL OPTIMIZATION : AN INTERNATIONAL JOURNAL DEALING WITH THEORETICAL AND COMPUTATIONAL ASPECTS OF SEEKING GLOBAL OPTIMA AND THEIR APPLICATIONS IN SCIENCE, MANAGEMENT AND ENGINEERING 2022; 83:3-28. [PMID: 35528138 PMCID: PMC9070988 DOI: 10.1007/s10898-021-01004-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/20/2021] [Indexed: 06/14/2023]
Abstract
Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.
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Affiliation(s)
| | - David Cowburn
- Departments of Biochemistry and of Physiology and Biophysics, Albert Einstein College of Medicine, NY 10461
| | - Yuehaw Khoo
- Department of Statistics, University of Chicago, IL 60637
| | - Amit Singer
- Department of Mathematics and PACM, Princeton University, NJ 08540
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31
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Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
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Affiliation(s)
- Dustin C. Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T. Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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32
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Structural and functional studies of LaIT2, an antimicrobial and insecticidal peptide from Liocheles australasiae. Toxicon 2022; 214:8-17. [DOI: 10.1016/j.toxicon.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022]
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33
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Gibson JM, Cui H, Ali MY, Zhao X, Debler EW, Zhao J, Trybus KM, Solmaz SR, Wang C. Coil-to-α-helix transition at the Nup358-BicD2 interface activates BicD2 for dynein recruitment. eLife 2022; 11:74714. [PMID: 35229716 PMCID: PMC8956292 DOI: 10.7554/elife.74714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Nup358, a protein of the nuclear pore complex, facilitates a nuclear positioning pathway that is essential for many biological processes, including neuromuscular and brain development. Nup358 interacts with the dynein adaptor Bicaudal D2 (BicD2), which in turn recruits the dynein machinery to position the nucleus. However, the molecular mechanisms of the Nup358/BicD2 interaction and the activation of transport remain poorly understood. Here for the first time, we show that a minimal Nup358 domain activates dynein/dynactin/BicD2 for processive motility on microtubules. Using nuclear magnetic resonance titration and chemical exchange saturation transfer, mutagenesis, and circular dichroism spectroscopy, a Nup358 α-helix encompassing residues 2162–2184 was identified, which transitioned from a random coil to an α-helical conformation upon BicD2 binding and formed the core of the Nup358-BicD2 interface. Mutations in this region of Nup358 decreased the Nup358/BicD2 interaction, resulting in decreased dynein recruitment and impaired motility. BicD2 thus recognizes Nup358 through a ‘cargo recognition α-helix,’ a structural feature that may stabilize BicD2 in its activated state and promote processive dynein motility.
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Affiliation(s)
- James M Gibson
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Heying Cui
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - M Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Xioaxin Zhao
- Department of Biological Sciences, Binghamton University, Binghamton, United States
| | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jing Zhao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Sozanne R Solmaz
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
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34
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Singh A, Martinez-Yamout MA, Wright PE, Dyson HJ. Interactions of a Long Noncoding RNA with Domains of NF-κB and IκBα: Implications for the Inhibition of Non-Signal-Related Phosphorylation. Biochemistry 2022; 61:367-376. [PMID: 35171557 PMCID: PMC8932344 DOI: 10.1021/acs.biochem.1c00732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transcription factor NF-κB is one of the central mediators of cellular signaling pathways. Under resting conditions, the canonical RelA-p50 (p65-p50) heterodimer NF-κB remains sequestered in the cytoplasm in complex with its inhibitor IκBα. Signal-mediated activation of NF-κB involves phosphorylation, ubiquitination and degradation of IκBα, and translocation of NF-κB to the nucleus. It was recently shown that a long noncoding RNA (termed NKILA) can modulate the NF-κB signaling circuit by interacting with the NF-κB-IκBα complex in the cytoplasm. In the current study, we investigated the interaction of RNA sequences derived from NKILA with domains of NF-κB and IκBα using NMR spectroscopy and native gel electrophoresis. Our results indicate that two RNA hairpin sequences interact with the DNA-binding domains of the Rel homology regions of RelA (p65) and p50 and that the same RNA sequences can affect the phosphorylation of the N-terminus of IκBα under low-salt conditions. We also observe that full-length RHR dimers (heterodimer of p65 and p50 and homodimer of p50) show a stronger interaction with the RNA hairpins than the individual domains of NF-κB. All of the interactions we observe between fragments of NKILA and domains of NF-κB are weak and nonspecific, consistent with the proposed function of the NKILA-NF-κB-IκBα interaction in protecting the NFκB-IκBα complex from aberrant activation of the NF-κB signaling pathway.
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35
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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36
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Chaves-Arquero B, Collins KM, Christodoulou E, Nicastro G, Martin SR, Ramos A. The distinct RNA-interaction modes of a small ZnF domain underlay TUT4(7) diverse action in miRNA regulation. RNA Biol 2021; 18:770-781. [PMID: 34719327 PMCID: PMC8782169 DOI: 10.1080/15476286.2021.1991169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
TUT4 and the closely related TUT7 are non-templated poly(U) polymerases required at different stages of development, and their mis-regulation or mutation has been linked to important cancer pathologies. While TUT4(7) interaction with its pre-miRNA targets has been characterized in detail, the molecular bases of the broader target recognition process are unclear. Here, we examine RNA binding by the ZnF domains of the protein. We show that TUT4(7) ZnF2 contains two distinct RNA binding surfaces that are used in the interaction with different RNA nucleobases in different targets, i.e that this small domain encodes diversity in TUT4(7) selectivity and molecular function. Interestingly and unlike other well-characterized CCHC ZnFs, ZnF2 is not physically coupled to the flanking ZnF3 and acts independently in miRNA recognition, while the remaining CCHC ZnF of TUT4(7), ZnF1, has lost its intrinsic RNA binding capability. Together, our data suggest that the ZnFs of TUT4(7) are independent units for RNA and, possibly, protein-protein interactions that underlay the protein's functional flexibility and are likely to play an important role in building its interaction network.
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Affiliation(s)
- Belén Chaves-Arquero
- Institute of Structural and Molecular Biology (ISMB) instead of (Ismb), University College London, London, UK
| | - Katherine M Collins
- Institute of Structural and Molecular Biology (ISMB) instead of (Ismb), University College London, London, UK
| | | | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology (ISMB) instead of (Ismb), University College London, London, UK
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37
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Medeiros J, Bamm VV, Jany C, Coackley C, Ward ME, Harauz G, Ryan SD, Ladizhansky V. Partial magic angle spinning NMR 1H, 13C, 15N resonance assignments of the flexible regions of a monomeric alpha-synuclein: conformation of C-terminus in the lipid-bound and amyloid fibril states. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:297-303. [PMID: 33797711 DOI: 10.1007/s12104-021-10020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Alpha-synuclein (α-syn) is a small presynaptic protein that is believed to play an important role in the pathogenesis of Parkinson's disease (PD). It localizes to presynaptic terminals where it partitions between a cytosolic soluble and a lipid-bound state. Recent evidence suggests that α-syn can also associate with mitochondrial membranes where it interacts with a unique anionic phospholipid cardiolipin (CL). Here, we examine the conformation of the flexible fragments of a monomeric α-syn bound to lipid vesicles composed of anionic 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipids, of tetraoleoyl CL (TOCL) and DOPC, and of fibrils. The dynamic properties of α-syn associated with DOPA:DOPC vesicles were the most favorable for conducting three-dimensional NMR experiments, and the 13C, 15N and amide 1H chemical shifts of the flexible and disordered C-terminus of α-syn could be assigned using three-dimensional through-bond magic angle spinning NMR spectroscopy. Although the C-terminus is more dynamically constrained in fibrils and in α-syn bound to TOCL:DOPC vesicles, a direct comparison of carbon chemical shifts detected using through bond two-dimensional spectroscopy indicates that the C-terminus is flexible and unstructured in all the three samples.
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Affiliation(s)
- Justin Medeiros
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Vladimir V Bamm
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Catherine Jany
- Department of Chemistry, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Carla Coackley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - George Harauz
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Scott D Ryan
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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38
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Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschlãger O, Bordusa F. Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:441-448. [PMID: 34415548 PMCID: PMC8481210 DOI: 10.1007/s12104-021-10043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Even though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these "unknown" proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the [Formula: see text]H, [Formula: see text]C, [Formula: see text]N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.
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Affiliation(s)
- Christoph Wiedemann
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry & Cluster of Excellence "Balance of the Microverse", Biostructural Interactions, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
| | - Kingsley Benjamin Obika
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Sandra Liebscher
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Jirschitzka
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Oliver Ohlenschlãger
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Frank Bordusa
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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39
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Baudin A, Xu X, Libich DS. The 1H, 15N and 13C resonance assignments of the C-terminal domain of Serpine mRNA binding protein 1 (SERBP1). BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:461-466. [PMID: 34436734 PMCID: PMC9990118 DOI: 10.1007/s12104-021-10046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
SERBP1 is a multifunctional mRNA-binding protein that has been shown to play a regulatory role in a number of biological processes such as thrombosis, DNA damage repair, and the cellular response to nutrient deprivation. Additionally, SERBP1 is upregulated in glioblastoma, leukemia as well as liver, prostrate and ovarian cancers where it has been implicated in metastatic disease and poor patient outcomes. SERBP1 binds target mRNA, stabilizing and regulating the post-translational expression of the transcript. Since SERBP1 lacks canonical RNA-binding motifs such as RRM domains or zinc fingers, its target recognition and binding mechanisms are not well understood. Recent reports suggest that it is capable of recognizing both RNA sequence motifs and structured domains. Here we report the production and purification of the intrinsically disordered C-terminal domain of SERBP1, the assignment of the 1H, 13C, 15N backbone resonances of the protein by solution-state NMR, and secondary structure predictions. We show that the protein is not entirely disordered and identify an α-helix that was stable under the experimental conditions. This work is the first step toward understanding the structural basis underpinning the molecular mechanisms of SERBP1 functions, particularly interactions with mRNA targets.
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Affiliation(s)
- Antoine Baudin
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - Xiaoping Xu
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA
| | - David S Libich
- Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
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40
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de Lourenço IO, Seixas FAV, Fernandez MA, Almeida FCL, Fossey MA, de Souza FP, Caruso ÍP. 1H, 15N, and 13C resonance assignments of the SH3-like tandem domain of human KIN protein. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:449-453. [PMID: 34417717 DOI: 10.1007/s12104-021-10044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
KIN is a DNA/RNA-binding protein conserved evolutionarily from yeast to humans and expressed ubiquitously in mammals. It is an essential nuclear protein involved in numerous cellular processes, such as DNA replication, class-switch recombination, cell cycle regulation, and response to UV or ionizing radiation-induced DNA damage. The C-terminal region of the human KIN (hKIN) protein is composed of an SH3-like tandem domain, which is crucial for the anti-proliferation effect of the full-length protein. Herein, we present the 1H, 15N, and 13C resonances assignment of the backbone and side chains for the SH3-like tandem domain of the hKIN protein, as well as the secondary structure prediction based on the assigned chemical shifts using TALOS-N software. This work prepares the ground for future studies of RNA-binding and backbone dynamics.
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Affiliation(s)
- Isabella Otenio de Lourenço
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, 15054-000, Brazil
| | | | - Maria Aparecida Fernandez
- Department of Biotechnology, Genetics and Cell Biology, Maringá State University (UEM), Maringá, PR, 87020-900, Brazil
| | - Fabio Ceneviva Lacerda Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil
| | - Marcelo Andrés Fossey
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, 15054-000, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, 15054-000, Brazil
| | - Ícaro Putinhon Caruso
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, 15054-000, Brazil.
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-590, Brazil.
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41
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Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Sci 2021; 30:2233-2245. [PMID: 34523753 DOI: 10.1002/pro.4184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/06/2022]
Abstract
HIV-1 capsid is comprised of over a hundred p24 protein molecules, arranged as either pentamers or hexamers. Three p24 mutants with amino acid substitutions in capsid N-terminal domain protein were examined: G60W (α3-4 loop), M68T (helix 4), and P90T (α4-5 loop), which exhibited no viability for biological activity. One common structural feature of the three p24 N-domain mutants, examined by NMR, was the long-range effect of more β-structures at the β2-strand in the N-terminal region compared with the wild-type. In addition, the presence of fewer helical structures was observed in M68T and P90T, beyond the broad area from helix 1 to the C-terminal part of helix 4. This suggests that both N-terminal beta structures and helices play important roles in the formation of p24 hexamers and pentamers. Next, compared with P90T, we examined cis-conformation or trans-conformation of wild-type adopted by isomerization at G89-P90. Since P90T mutant adopts only a trans-conformation, comparison of chemical shifts and signal intensities between each spectra revealed that the major peaks (about 85%) in the spectrum of wild-type correspond to trans-conformation. Furthermore, it was indicated that the region in cis-conformation (minor; 15%) was more stabilized than that observed in trans-conformation, based on the analyses of heteronuclear Overhauser effect as well as the order-parameter. Therefore, it was concluded that the cis-conformation is more favorable than the trans-conformation for the interaction between the p24 N-terminal domain and cyclophilin-A. This is because HIV-1 with a P90T protein, which adopts only a trans-conformation, is associated with non-viability of biological activity.
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Affiliation(s)
- Yusuke Sato
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center (RSC), Yokohama, Japan
| | - Satoru Watanabe
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems, Dynamics Research, Yokohama, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center (RSC), Yokohama, Japan
| | - Munehito Arai
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems, Dynamics Research, Yokohama, Japan.,School of Computing, Tokyo Institute of Technology, Yokohama, Japan
| | - Chiaki Nishimura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Japan
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42
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Singh A, Fenwick RB, Dyson HJ, Wright PE. Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase. Biochemistry 2021; 60:2663-2671. [PMID: 34428034 DOI: 10.1021/acs.biochem.1c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational fluctuations from ground-state to sparsely populated but functionally important excited states play a key role in enzyme catalysis. For Escherichia coli dihydrofolate reductase (DHFR), the release of the product tetrahydrofolate (THF) and oxidized cofactor NADP+ occurs through exchange between closed and occluded conformations of the Met20 loop. A "dynamic knockout" mutant of E. coli DHFR, where the E. coli sequence in the Met20 loop is replaced by the human sequence (N23PP/S148A), models human DHFR and is incapable of accessing the occluded conformation. 1H and 15N CPMG relaxation dispersion analysis for the ternary product complex of the mutant enzyme with NADP+ and the product analogue 5,10-dideazatetrahydrofolate (ddTHF) (E:ddTHF:NADP+) reveals the mechanism by which NADP+ is released when the Met20 loop cannot undergo the closed-to-occluded conformational transition. Two excited states were observed: one related to a faster, relatively high-amplitude conformational fluctuation in areas near the active site, associated with the shuttling of the nicotinamide ring of the cofactor out of the active site, and the other to a slower process where ddTHF undergoes small-amplitude motions within the binding site that are consistent with disorder observed in a room-temperature X-ray crystal structure of the N23PP/S148A mutant protein. These motions likely arise due to steric conflict of the pterin ring of ddTHF with the ribose-nicotinamide moiety of NADP+ in the closed active site. These studies demonstrate that site-specific kinetic information from relaxation dispersion experiments can provide intimate details of the changes in catalytic mechanism that result from small changes in local amino acid sequence.
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Affiliation(s)
- Amrinder Singh
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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43
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Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins 2021; 90:96-109. [PMID: 34312913 PMCID: PMC9290662 DOI: 10.1002/prot.26189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.
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Affiliation(s)
- Heike I Rösner
- BRIC, University of Copenhagen, Copenhagen N, Denmark.,Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Martina Caldarini
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy
| | - Gregory Potel
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Daniel Malmodin
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Maria A Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Ricardo A Broglia
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Niels Bohr Institutet, University of Copenhagen, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Guido Tiana
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Center for Complexity and Biosystems, Università degli Studi di Milano, Milan, Italy
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44
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Goenaga Infante H, Warren J, Chalmers J, Dent G, Todoli JL, Collingwood J, Telling N, Resano M, Limbeck A, Schoenberger T, Hibbert DB, LeGresley A, Adams K, Craston D. Glossary of methods and terms used in analytical spectroscopy (IUPAC Recommendations 2019). PURE APPL CHEM 2021. [DOI: 10.1515/pac-2019-0203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Recommendations are given concerning the terminology of concepts and methods used in spectroscopy in analytical chemistry, covering nuclear magnetic resonance spectroscopy, atomic spectroscopy, and vibrational spectroscopy.
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Affiliation(s)
| | | | | | | | - Jose Luis Todoli
- Department of Analytical Chemistry , University of Alicante , Alicante , Spain
| | | | - Neil Telling
- School of Pharmacy and Bioengineering, Keele University , Stoke on Trent , UK
| | - Martin Resano
- Department of Analytical Chemistry , University of Zaragoza , Zaragoza , Spain
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics , Vienna , Austria
| | | | | | - Adam LeGresley
- Department of Chemical and Pharmaceutical Sciences , Kingston University , Kingston-upon-Thames , UK
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45
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Moran MW, Ramirez EP, Zook JD, Saarinen AM, Baravati B, Goode MR, Laloudakis V, Kaschner EK, Olson TL, Craciunescu FM, Hansen DT, Liu J, Fromme P. Biophysical characterization and a roadmap towards the NMR solution structure of G0S2, a key enzyme in non-alcoholic fatty liver disease. PLoS One 2021; 16:e0249164. [PMID: 34260600 PMCID: PMC8279337 DOI: 10.1371/journal.pone.0249164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/13/2021] [Indexed: 11/19/2022] Open
Abstract
In the United States non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease, affecting an estimated 80 to 100 million people. It occurs in every age group, but predominantly in people with risk factors such as obesity and type 2 diabetes. NAFLD is marked by fat accumulation in the liver leading to liver inflammation, which may lead to scarring and irreversible damage progressing to cirrhosis and liver failure. In animal models, genetic ablation of the protein G0S2 leads to alleviation of liver damage and insulin resistance in high fat diets. The research presented in this paper aims to aid in rational based drug design for the treatment of NAFLD by providing a pathway for a solution state NMR structure of G0S2. Here we describe the expression of G0S2 in an E. coli system from two different constructs, both of which are confirmed to be functionally active based on the ability to inhibit the activity of Adipose Triglyceride Lipase. In one of the constructs, preliminary NMR spectroscopy measurements show dominant alpha-helical characteristics as well as resonance assignments on the N-terminus of G0S2, allowing for further NMR work with this protein. Additionally, the characterization of G0S2 oligomers are outlined for both constructs, suggesting that G0S2 may defensively exist in a multimeric state to protect and potentially stabilize the small 104 amino acid protein within the cell. This information presented on the structure of G0S2 will further guide future development in the therapy for NAFLD.
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Affiliation(s)
- Michael W. Moran
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Elizabeth P. Ramirez
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - James D. Zook
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
| | - Alicia M. Saarinen
- Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona Scottsdale, AZ, United States of America
- Department of Cardiovascular Medicine, Mayo Clinic in Arizona Scottsdale, AZ, United States of America
| | - Bobby Baravati
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Matthew R. Goode
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Vasiliki Laloudakis
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
| | - Emily K. Kaschner
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Tien L. Olson
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Felicia M. Craciunescu
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
| | - Debra T. Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- Biodesign Center for Innovations in Medicine, Arizona State University, Tempe, AZ, United States of America
| | - Jun Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
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46
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Onofrei D, Stengel D, Jia D, Johnson HR, Trescott S, Soni A, Addison B, Muthukumar M, Holland GP. Investigating the Atomic and Mesoscale Interactions that Facilitate Spider Silk Protein Pre-Assembly. Biomacromolecules 2021; 22:3377-3385. [PMID: 34251190 DOI: 10.1021/acs.biomac.1c00473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Black widow spider dragline silk is one of nature's high-performance biological polymers, exceeding the strength and toughness of most man-made materials including high tensile steel and Kevlar. Major ampullate (Ma), or dragline silk, is primarily comprised of two spidroin proteins (Sp) stored within the Ma gland. In the native gland environment, the MaSp1 and MaSp2 proteins self-associate to form hierarchical 200-300 nm superstructures despite being intrinsically disordered proteins (IDPs). Here, dynamic light scattering (DLS), three-dimensional (3D) triple resonance solution NMR, and diffusion NMR is utilized to probe the MaSp size, molecular structure, and dynamics of these protein pre-assemblies diluted in 4 M urea and identify specific regions of the proteins important for silk protein pre-assembly. 3D NMR indicates that the Gly-Ala-Ala and Ala-Ala-Gly motifs flanking the poly(Ala) runs, which comprise the β-sheet forming domains in fibers, are perturbed by urea, suggesting that these regions may be important for silk protein pre-assembly stabilization.
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Affiliation(s)
- David Onofrei
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Dillan Stengel
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Di Jia
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hannah R Johnson
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Samantha Trescott
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Ashana Soni
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Bennett Addison
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-1030, United States
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47
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Structure of Nanobody Nb23. Molecules 2021; 26:molecules26123567. [PMID: 34207949 PMCID: PMC8230604 DOI: 10.3390/molecules26123567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.
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48
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Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. JACS AU 2021; 1:484-500. [PMID: 34467311 PMCID: PMC8395690 DOI: 10.1021/jacsau.0c00094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 06/13/2023]
Abstract
Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to proteins and how these effects might propagate beyond the immediate neighborhood of the binding site. Here, we investigate this question by introducing minor changes in ligand structure and characterizing the effects of these on ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and computational approaches including molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). We studied a congeneric series of ligands with a fluorophenyl-triazole moiety, where the fluorine substituent varies between the ortho, meta, and para positions (denoted O, M, and P). The M and P ligands have similar affinities, whereas the O ligand has 3-fold lower affinity, reflecting differences in binding enthalpy and entropy. The results reveal surprising differences in conformational and solvation entropy among the three complexes. NMR backbone order parameters show that the O-bound protein has reduced conformational entropy compared to the M and P complexes. By contrast, the bound ligand is more flexible in the O complex, as determined by 19F NMR relaxation, ensemble-refined X-ray diffraction data, and MD simulations. Furthermore, GIST calculations indicate that the O-bound complex has less unfavorable solvation entropy compared to the other two complexes. Thus, the results indicate compensatory effects from ligand conformational entropy and water entropy, on the one hand, and protein conformational entropy, on the other hand. Taken together, these different contributions amount to entropy-entropy compensation among the system components involved in ligand binding to a target protein.
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Affiliation(s)
- Johan Wallerstein
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | | | - Rohit Kumar
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Octav Caldararu
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Kristoffer Peterson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sven Wernersson
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulrika Brath
- The
Swedish NMR Center, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hakon Leffler
- Microbiology,
Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, 221 00 Lund, Sweden
| | - Esko Oksanen
- European
Spallation Source ESS ERIC, 225 92 Lund, Sweden
| | - Derek T. Logan
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf Ryde
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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49
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Karjalainen M, Hellman M, Tossavainen H, Permi P. 1H, 13C, and 15N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:213-217. [PMID: 33475933 PMCID: PMC7973643 DOI: 10.1007/s12104-021-10008-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
LEE-encoded effector EspF (EspF) is an effector protein part of enteropathogenic Escherichia coli's (EPEC's) arsenal for intestinal infection. This intrinsically disordered protein contains three highly conserved repeats which together compose over half of the protein's complete amino acid sequence. EPEC uses EspF to hijack host proteins in order to promote infection. In the attack EspF is translocated, together with other effector proteins, to host cell via type III secretion system. Inside host EspF stimulates actin polymerization by interacting with Neural Wiskott-Aldrich syndrome protein (N-WASP), a regulator in actin polymerization machinery. It is presumed that EspF acts by disrupting the autoinhibitory state of N-WASP GTPase binding domain. In this NMR spectroscopy study, we report the 1H, 13C, and 15N resonance assignments for the complex formed by the first 47-residue repeat of EspF and N-WASP GTPase binding domain. These near-complete resonance assignments provide the basis for further studies which aim to characterize structure, interactions, and dynamics between these two proteins in solution.
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Affiliation(s)
- Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.
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D'Andréa ÉD, Retel JS, Diehl A, Schmieder P, Oschkinat H, Pires JR. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. J Struct Biol 2021; 213:107715. [PMID: 33705979 DOI: 10.1016/j.jsb.2021.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The 106-residue protein Q4DY78 (UniProt accession number) from Trypanosoma cruzi is highly conserved in the related kinetoplastid pathogens Trypanosoma brucei and Leishmania major. Given the essentiality of its orthologue in T. brucei, the high sequence conservation with other trypanosomatid proteins, and the low sequence similarity with mammalian proteins, Q4DY78 is an attractive protein for structural characterization. Here, we solved the structure of Q4DY78 by solution NMR and evaluated its backbone dynamics. Q4DY78 is composed of five α -helices and a small, two-stranded antiparallel β-sheet. The backbone RMSD is 0.22 ± 0.05 Å for the representative ensemble of the 20 lowest-energy structures. Q4DY78 is overall rigid, except for N-terminal residues (V8 to I10), residues at loop 4 (K57 to G65) and residues at the C-terminus (F89 to F112). Q4DY78 has a short motif FPCAP that could potentially mediate interactions with the host cytoskeleton via interaction with EVH1 (Drosophila Enabled (Ena)/Vasodilator-stimulated phosphoprotein (VASP) homology 1) domains. Albeit Q4DY78 lacks calcium-binding motifs, its fold resembles that of eukaryotic calcium-binding proteins such as calcitracin, calmodulin, and polcacin Bet V4. We characterized this novel protein with a calcium binding fold without the capacity to bind calcium.
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Affiliation(s)
- Éverton Dias D'Andréa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil
| | - Joren Sebastian Retel
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Anne Diehl
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany; Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, Berlin 14195, Germany
| | - José Ricardo Pires
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil.
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