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Takayesu A, Mahoney BJ, Goring AK, Jessup T, Ogorzalek Loo RR, Loo JA, Clubb RT. Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum. Proteins 2024; 92:946-958. [PMID: 38597224 PMCID: PMC11222046 DOI: 10.1002/prot.26690] [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: 11/06/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass-sensing RsgI-type anti-σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti-σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn-Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti-σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.
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Affiliation(s)
- Allen Takayesu
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Brendan J. Mahoney
- UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- Molecular Biology Institute. University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Tobie Jessup
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- Molecular Biology Institute. University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- Molecular Biology Institute. University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
- Molecular Biology Institute. University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
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2
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Bhattacharya S, Varney KM, Dahmane T, Johnson BA, Weber DJ, Palmer AG. Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00443-w. [PMID: 38856928 DOI: 10.1007/s10858-024-00443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/27/2024] [Indexed: 06/11/2024]
Abstract
Deuterium (2H) spin relaxation of 13CH2D methyl groups has been widely applied to investigate picosecond-to-nanosecond conformational dynamics in proteins by solution-state NMR spectroscopy. The B0 dependence of the 2H spin relaxation rates is represented by a linear relationship between the spectral density function at three discrete frequencies J(0), J(ωD) and J(2ωD). In this study, the linear relation between 2H relaxation rates at B0 fields separated by a factor of two and the interpolation of rates at intermediate frequencies are combined for a more robust approach for spectral density mapping. The general usefulness of the approach is demonstrated on a fractionally deuterated (55%) and alternate 13C-12C labeled sample of E. coli RNase H. Deuterium relaxation rate constants (R1, R1ρ, RQ, RAP) were measured for 57 well-resolved 13CH2D moieties in RNase H at 1H frequencies of 475 MHz, 500 MHz, 900 MHz, and 950 MHz. The spectral density mapping of the 475/950 MHz data combination was performed independently and jointly to validate the expected relationship between data recorded at B0 fields separated by a factor of two. The final analysis was performed by jointly analyzing 475/950 MHz rates with 700 MHz rates interpolated from 500/900 MHz data to yield six J(ωD) values for each methyl peak. The J(ω) profile for each peak was fit to the original (τM, Sf2, τf) or extended model-free function (τM, Sf2, Ss2, τf, τs) to obtain optimized dynamic parameters.
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Affiliation(s)
| | - Kristen M Varney
- University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA
| | - Tassadite Dahmane
- New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - David J Weber
- University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA
| | - Arthur G Palmer
- New York Structural Biology Center, 89 Convent Ave, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY, 10032, USA.
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3
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González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
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Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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4
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Freise C, Zappe A, Löwa N, Schnorr J, Pagel K, Wiekhorst F, Taupitz M. Uremic Toxin-Induced Exosome-like Extracellular Vesicles Contain Enhanced Levels of Sulfated Glycosaminoglycans which Facilitate the Interaction with Very Small Superparamagnetic Iron Oxide Particles. Int J Mol Sci 2023; 24:14253. [PMID: 37762555 PMCID: PMC10532171 DOI: 10.3390/ijms241814253] [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: 08/14/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Uremic toxins exert pathophysiological effects on cells and tissues, such as the generation of a pro-calcifying subtype of exosome-like extracellular vesicles (EVs) in vascular cells. Little is known about the effects of the toxins on the surface structure of EVs. Thus, we studied the effects of uremic toxins on the abundance of sulfated glycosaminoglycans (GAGs) in EVs, and the implications for binding of ligands such as very small superparamagnetic iron oxide particles (VSOPs) which could be of relevance for radiological EV-imaging. Vascular cells were treated with the uremic toxins NaH2PO4 and a mixture of urea and indoxyl sulfate. Uremia in rats was induced by adenine feeding. EVs were isolated from culture supernatants and plasma of rats. By proton T1-relaxometry, magnetic particle spectroscopy, and analysis of genes, proteins, and GAG-contents, we analyzed the roles of GAGs in the ligand binding of EVs. By influencing GAG-associated genes in host cells, uremic toxins induced higher GAG contents in EVs, particularly of sulfated chondroitin sulfate and heparan sulfate chains. EVs with high GAG content interacted stronger with VSOPs compared to control ones. This was confirmed by experiments with GAG-depleted EVs from genetically modified CHO cells and with uremic rat-derived EVs. Mechanistically, uremic toxin-induced PI3K/AKT-signaling and expression of the sulfate transporter SLC26A2 in host cells contributed to high GAG contents in EVs. In conclusion, uremic conditions induce enhanced GAG contents in EVs, which entails a stronger interaction with VSOPs. VSOPs might be suitable for radiological imaging of EVs rich in GAGs.
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Affiliation(s)
- Christian Freise
- Department of Radiology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (J.S.); (M.T.)
| | - Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Altensteinstraße 23A, 14195 Berlin, Germany; (A.Z.); (K.P.)
| | - Norbert Löwa
- Metrology for Magnetic Nanoparticles Berlin, Physikalisch-Technische Bundesanstalt Berlin, Abbestr. 2, 10587 Berlin, Germany; (N.L.); (F.W.)
| | - Jörg Schnorr
- Department of Radiology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (J.S.); (M.T.)
| | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Altensteinstraße 23A, 14195 Berlin, Germany; (A.Z.); (K.P.)
| | - Frank Wiekhorst
- Metrology for Magnetic Nanoparticles Berlin, Physikalisch-Technische Bundesanstalt Berlin, Abbestr. 2, 10587 Berlin, Germany; (N.L.); (F.W.)
| | - Matthias Taupitz
- Department of Radiology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; (J.S.); (M.T.)
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5
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Pressure, motion, and conformational entropy in molecular recognition by proteins. BIOPHYSICAL REPORTS 2022; 3:100098. [PMID: 36647534 PMCID: PMC9840116 DOI: 10.1016/j.bpr.2022.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century, detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. More recently, a dynamical proxy based on NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. Here, we report the pressure dependence of fast internal motion within the ribonuclease barnase and its complex with the protein barstar. In what we believe is a first example, we find that protein dynamics are conserved along the pressure-binding thermodynamic cycle. The femtomolar affinity of the barnase-barstar complex exists despite a penalty by -TΔSconf of +11.7 kJ/mol at ambient pressure. At high pressure, however, the overall change in side-chain dynamics is zero, and binding occurs with no conformational entropy penalty, suggesting an important role of conformational dynamics in the adaptation of protein function to extreme environments. Distinctive clustering of the pressure sensitivity is observed in response to both pressure and binding, indicating the presence of conformational heterogeneity involving less efficiently packed alternative conformation(s). The structural segregation of dynamics observed in barnase is striking and shows how changes in both the magnitude and the sign of regional contributions of conformational entropy to the thermodynamics of protein function are possible.
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6
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Olivieri C, Li GC, Wang Y, V.S. M, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia G. ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy. SCIENCE ADVANCES 2022; 8:eabo0696. [PMID: 35905186 PMCID: PMC9337769 DOI: 10.1126/sciadv.abo0696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
ATP-competitive inhibitors are currently the largest class of clinically approved drugs for protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic activity, preventing substrate phosphorylation. A problem with these drugs, however, is that inhibited kinases may still recognize and bind downstream substrates, acting as scaffolds or binding hubs for signaling partners. Here, using protein kinase A as a model system, we show that chemically different ATP-competitive inhibitors modulate the substrate binding cooperativity by tuning the conformational entropy of the kinase and shifting the populations of its conformationally excited states. Since we found that binding cooperativity and conformational entropy of the enzyme are correlated, we propose a new paradigm for the discovery of ATP-competitive inhibitors, which is based on their ability to modulate the allosteric coupling between nucleotide and substrate-binding sites.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Geoffrey C. Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Manu V.S.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Alfonso De Simone
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Napoli 80131, Italy
| | | | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, and Pharmacology, University of California at San Diego, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Selvaraj C, Rudhra O, Alothaim AS, Alkhanani M, Singh SK. Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:59-83. [PMID: 35534116 DOI: 10.1016/bs.apcsb.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Ondipilliraja Rudhra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Mustfa Alkhanani
- Emergency Service Department, College of Applied Sciences, Al Maarefa University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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8
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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9
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Waudby C, Christodoulou J. Analysis of conformational exchange processes using methyl-TROSY-based Hahn echo measurements of quadruple-quantum relaxation. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:777-793. [PMID: 37905227 PMCID: PMC10583286 DOI: 10.5194/mr-2-777-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 11/02/2023]
Abstract
Transverse nuclear spin relaxation is a sensitive probe of chemical exchange on timescales on the order of microseconds to milliseconds. Here we present an experiment for the simultaneous measurement of the relaxation rates of two quadruple-quantum transitions in 13 CH3 -labelled methyl groups. These coherences are protected against relaxation by intra-methyl dipolar interactions and so have unexpectedly long lifetimes within perdeuterated biomacromolecules. However, these coherences also have an order of magnitude higher sensitivity to chemical exchange broadening than lower order coherences and therefore provide ideal probes of dynamic processes. We show that analysis of the static magnetic field dependence of zero-, double- and quadruple-quantum Hahn echo relaxation rates provides a robust indication of chemical exchange and can determine the signed relative magnitudes of proton and carbon chemical shift differences between ground and excited states. We also demonstrate that this analysis can be combined with established Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements, providing improved precision in parameter estimates, particularly in the determination of 1 H chemical shift differences.
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Affiliation(s)
- Christopher A. Waudby
- Institute of Structural and Molecular Biology, University College
London, London, WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College
London, London, WC1E 6BT, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
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10
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Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
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Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
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11
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Beckwith MA, Erazo-Colon T, Johnson BA. RING NMR dynamics: software for analysis of multiple NMR relaxation experiments. JOURNAL OF BIOMOLECULAR NMR 2021; 75:9-23. [PMID: 33098475 PMCID: PMC7897199 DOI: 10.1007/s10858-020-00350-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/23/2020] [Indexed: 05/05/2023]
Abstract
Molecular motions are fundamental to the existence of life, and NMR spectroscopy remains one of the most useful and powerful methods to measure their rates and molecular characteristics. Multiple experimental methods are available for measuring the NMR relaxation properties and these can require different methods for extracting model parameters. We present here a new software application, RING NMR Dynamics, that is designed to support analysis of multiple relaxation types. The initial release of RING NMR Dynamics supports the analysis of exponential decay experiments such as T1 and T2, as well as CEST and R2 and R1ρ relaxation dispersion. The software runs on multiple operating systems in both a command line mode and a user-friendly GUI that allows visualizing and simulating relaxation data. Interaction with another program, NMRFx Analyst, allows drilling down from the derived relaxation parameters to the raw spectral data.
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Affiliation(s)
- Martha A Beckwith
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Teddy Erazo-Colon
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
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12
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Kharchenko V, Nowakowski M, Jaremko M, Ejchart A, Jaremko Ł. Dynamic 15N{ 1H} NOE measurements: a tool for studying protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:707-716. [PMID: 32918646 PMCID: PMC7701129 DOI: 10.1007/s10858-020-00346-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.
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Affiliation(s)
- Vladlena Kharchenko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michal Nowakowski
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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13
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Marques BS, Stetz MA, Jorge C, Valentine KG, Wand AJ, Nucci NV. Protein conformational entropy is not slaved to water. Sci Rep 2020; 10:17587. [PMID: 33067552 PMCID: PMC7567893 DOI: 10.1038/s41598-020-74382-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.
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Affiliation(s)
- Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Stetz
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine Jorge
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen G Valentine
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77845-2128, USA.
| | - Nathaniel V Nucci
- Department of Physics and Astronomy and Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ, 08028, USA.
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14
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O'Brien ES, Fuglestad B, Lessen HJ, Stetz MA, Lin DW, Marques BS, Gupta K, Fleming KG, Wand AJ. Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy. Angew Chem Int Ed Engl 2020; 59:11108-11114. [PMID: 32277554 PMCID: PMC7318686 DOI: 10.1002/anie.202003527] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Indexed: 12/31/2022]
Abstract
The internal motions of integral membrane proteins have largely eluded comprehensive experimental characterization. Here the fast side-chain dynamics of the α-helical sensory rhodopsin II and the β-barrel outer membrane protein W have been investigated in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Despite their differing topologies, both proteins have a similar distribution of methyl-bearing side-chain motion that is largely independent of membrane mimetic. The methyl-bearing side chains of both proteins are, on average, more dynamic in the ps-ns timescale than any soluble protein characterized to date. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect. Furthermore, the high conformational entropy could greatly influence the thermodynamics underlying membrane-protein functions, including ligand binding, allostery, and signaling.
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Affiliation(s)
- Evan S. O'Brien
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Brian Fuglestad
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
- Present address: Department of ChemistryVirginia Commonwealth UniversityRichmondVA23284USA
| | - Henry J. Lessen
- Department of BiophysicsJohns Hopkins UniversityBaltimoreMD21218USA
| | - Matthew A. Stetz
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Danny W. Lin
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Bryan S. Marques
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Kushol Gupta
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Karen G. Fleming
- Department of BiophysicsJohns Hopkins UniversityBaltimoreMD21218USA
| | - A. Joshua Wand
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTX77843USA
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
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15
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O'Brien ES, Fuglestad B, Lessen HJ, Stetz MA, Lin DW, Marques BS, Gupta K, Fleming KG, Wand AJ. Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Evan S. O'Brien
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Brian Fuglestad
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
- Present address: Department of Chemistry Virginia Commonwealth University Richmond VA 23284 USA
| | - Henry J. Lessen
- Department of Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - Matthew A. Stetz
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Danny W. Lin
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Bryan S. Marques
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Kushol Gupta
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Karen G. Fleming
- Department of Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - A. Joshua Wand
- Department of Biochemistry & Biophysics Texas A&M University College Station TX 77843 USA
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
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16
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Bibow S. Exploring Lipid and Membrane Protein Dynamics Using Lipid-Bilayer Nanodiscs and Solution-State NMR Spectroscopy. Methods Mol Biol 2020; 2127:397-419. [PMID: 32112335 DOI: 10.1007/978-1-0716-0373-4_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The relationship of membrane protein function and the surrounding lipid bilayer goes far beyond simple hydrophobic interactions. At least from the 1980s, it is speculated that a certain fluid lipid state may be important not only for the lateral diffusion of membrane proteins (MPs) but also for modulating the catalytic activity of MPs (Lenaz. Bioscience Rep 7 (11):823-837, 1987). Indeed, acyl chain length, hydrophobic mismatch, and lipid headgroups are determinants for enzymatic and transport activities of MPs (Dumas et al. Biochemistry 39(16):4846-4854, 2000; Johannsson et al. Biochim Biophys Acta 641(2):416-421, 1981; Montecucco et al. FEBS Lett 144(1):145-148, 1982; Martens et al. Nat Struct Mol Biol 23(8):744-751, 2016). Moreover, it is speculated that changes in membrane lipid dynamics are important in the field of thermosensation (Vriens J, Nilius B, Voets T, Nat Rev Neurosci 15:573-589, 2014). Atomic insights into lipid-mediated modulation of membrane protein dynamics would therefore provide new insights with the potential to fundamentally extend our understanding on dynamic lipid-protein interdependencies.This chapter describes the expression and purification of nanodiscs assembled from membrane scaffold protein (MSP) as well as the expression and purification of the outer membrane protein X (OmpX). Subsequently, the incorporation of OmpX into MSP-derived nanodiscs is explained in detail. The chapter concludes with the setup of nuclear magnetic resonance (NMR) relaxation experiments and the extraction of relaxation rates for OmpX and the surrounding lipids.
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Affiliation(s)
- Stefan Bibow
- Biozentrum, University of Basel, Basel, Switzerland.
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17
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Bibow S. Opportunities and Challenges of Backbone, Sidechain, and RDC Experiments to Study Membrane Protein Dynamics in a Detergent-Free Lipid Environment Using Solution State NMR. Front Mol Biosci 2019; 6:103. [PMID: 31709261 PMCID: PMC6823230 DOI: 10.3389/fmolb.2019.00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022] Open
Abstract
Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.
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Affiliation(s)
- Stefan Bibow
- Biozentrum, University of Basel, Basel, Switzerland
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