1
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Marques S, Kouba P, Legrand A, Sedlar J, Disson L, Planas-Iglesias J, Sanusi Z, Kunka A, Damborsky J, Pajdla T, Prokop Z, Mazurenko S, Sivic J, Bednar D. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU 2024; 4:2228-2245. [PMID: 38938816 PMCID: PMC11200249 DOI: 10.1021/jacsau.4c00182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework to quantify changes in the conformational distribution and dynamics of a disordered biomolecule in the presence and absence of small organic drug candidate molecules. First, molecular dynamics trajectories are generated using enhanced sampling, in the presence and absence of small molecule drug candidates, and ensembles of soft Markov state models (MSMs) are learned for each system using unsupervised machine learning. Second, these ensembles of learned MSMs are aligned across different systems based on a solution to an optimal transport problem. Third, the directional importance of inter-residue distances for the assignment to different conformational states is assessed by a discriminative analysis of aggregated neural network gradients. This final step provides interpretability and biophysical context to the learned MSMs. We applied this novel computational framework to assess the effects of ongoing phase 3 therapeutics tramiprosate (TMP) and its metabolite 3-sulfopropanoic acid (SPA) on the disordered Aβ42 peptide involved in Alzheimer's disease. Based on adaptive sampling molecular dynamics and CoVAMPnet analysis, we observed that both TMP and SPA preserved more structured conformations of Aβ42 by interacting nonspecifically with charged residues. SPA impacted Aβ42 more than TMP, protecting α-helices and suppressing the formation of aggregation-prone β-strands. Experimental biophysical analyses showed only mild effects of TMP/SPA on Aβ42 and activity enhancement by the endogenous metabolization of TMP into SPA. Our data suggest that TMP/SPA may also target biomolecules other than Aβ peptides. The CoVAMPnet method is broadly applicable to study the effects of drug candidates on the conformational behavior of intrinsically disordered biomolecules.
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Affiliation(s)
- Sérgio
M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Petr Kouba
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
- Faculty
of Electrical Engineering, Czech Technical
University in Prague, Technicka 2, Dejvice, Praha 6 166 27, Czech Republic
| | - Anthony Legrand
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Jiri Sedlar
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Lucas Disson
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Zainab Sanusi
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Antonin Kunka
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Tomas Pajdla
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Josef Sivic
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
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2
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Sharma P, Maklashina E, Voehler M, Balintova S, Dvorakova S, Kraus M, Hadrava Vanova K, Nahacka Z, Zobalova R, Boukalova S, Cunatova K, Mracek T, Ghayee HK, Pacak K, Rohlena J, Neuzil J, Cecchini G, Iverson TM. Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners. Nat Commun 2024; 15:473. [PMID: 38212624 PMCID: PMC10784507 DOI: 10.1038/s41467-023-44563-7] [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: 11/29/2022] [Accepted: 12/19/2023] [Indexed: 01/13/2024] Open
Abstract
Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Markus Voehler
- Department of Chemistry Vanderbilt University, Nashville, TN, 37232, USA
- Center for Structural Biology Vanderbilt University, Nashville, TN, 37232, USA
| | - Sona Balintova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
- Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic
| | - Sarka Dvorakova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Michal Kraus
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Katerina Hadrava Vanova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Zuzana Nahacka
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Renata Zobalova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Stepana Boukalova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Kristyna Cunatova
- Institute of Physiology, Czech Academy of Sciences, Prague 4, 142 20, Prague, Czech Republic
| | - Tomas Mracek
- Institute of Physiology, Czech Academy of Sciences, Prague 4, 142 20, Prague, Czech Republic
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology & Metabolism, University of Florida College of Medicine and Malcom Randall, VA Medical Center, Gainesville, FL, 32608, USA
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic.
- Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic.
- School of Pharmacy and Medical Science, Griffith University, Southport, QLD, 4222, Australia.
- 1st Faculty of Medicine, Charles University, 128 00, Prague 2, Czech Republic.
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Center for Structural Biology Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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3
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Fenton M, Gregory E, Daughdrill G. Protein disorder and autoinhibition: The role of multivalency and effective concentration. Curr Opin Struct Biol 2023; 83:102705. [PMID: 37778184 PMCID: PMC10841074 DOI: 10.1016/j.sbi.2023.102705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this review, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence conservation varies from high to low. In some cases, identifiable motifs that are essential for autoinhibition remain intact within a rapidly evolving sequence, over long evolutionary distances. Finally, we examine the potential of AlphaFold2 to predict autoinhibitory intramolecular interactions involving IDRs.
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Affiliation(s)
- Malissa Fenton
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Gregory
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Gary Daughdrill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
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4
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Amith W, Dutagaci B. Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation. J Phys Chem B 2023; 127:9223-9235. [PMID: 37870995 PMCID: PMC10626582 DOI: 10.1021/acs.jpcb.3c02655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.
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Affiliation(s)
- Weththasinghage
D. Amith
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
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5
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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6
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Perera BLA, Colina CM. Cluster formation of initiators as a tool to impose conformational stability to unstructured regions of a protein. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1963000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- B. Lakshitha A. Perera
- Department of Chemistry, University of Florida, Gainesville, FL, USA
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL, USA
- Center for Macromolecular Science and Engineering, University of Florida, Gainesville, FL, USA
| | - Coray M. Colina
- Department of Chemistry, University of Florida, Gainesville, FL, USA
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL, USA
- Center for Macromolecular Science and Engineering, University of Florida, Gainesville, FL, USA
- Department of Material Science and Engineering, University of Florida, Gainesville, FL, USA
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7
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Pérez Y, Bonet R, Corredor M, Domingo C, Moure A, Messeguer À, Bujons J, Alfonso I. Semaphorin 3A-Glycosaminoglycans Interaction as Therapeutic Target for Axonal Regeneration. Pharmaceuticals (Basel) 2021; 14:ph14090906. [PMID: 34577606 PMCID: PMC8465649 DOI: 10.3390/ph14090906] [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: 08/04/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Semaphorin 3A (Sema3A) is a cell-secreted protein that participates in the axonal guidance pathways. Sema3A acts as a canonical repulsive axon guidance molecule, inhibiting CNS regenerative axonal growth and propagation. Therefore, interfering with Sema3A signaling is proposed as a therapeutic target for achieving functional recovery after CNS injuries. It has been shown that Sema3A adheres to the proteoglycan component of the extracellular matrix (ECM) and selectively binds to heparin and chondroitin sulfate-E (CS-E) glycosaminoglycans (GAGs). We hypothesize that the biologically relevant interaction between Sema3A and GAGs takes place at Sema3A C-terminal polybasic region (SCT). The aims of this study were to characterize the interaction of the whole Sema3A C-terminal polybasic region (Sema3A 725–771) with GAGs and to investigate the disruption of this interaction by small molecules. Recombinant Sema3A basic domain was produced and we used a combination of biophysical techniques (NMR, SPR, and heparin affinity chromatography) to gain insight into the interaction of the Sema3A C-terminal domain with GAGs. The results demonstrate that SCT is an intrinsically disordered region, which confirms that SCT binds to GAGs and helps to identify the specific residues involved in the interaction. NMR studies, supported by molecular dynamics simulations, show that a new peptoid molecule (CSIC02) may disrupt the interaction between SCT and heparin. Our structural study paves the way toward the design of new molecules targeting these protein–GAG interactions with potential therapeutic applications.
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Affiliation(s)
- Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- Correspondence: (Y.P.); (I.A.)
| | - Roman Bonet
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Miriam Corredor
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Cecilia Domingo
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Alejandra Moure
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Àngel Messeguer
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Jordi Bujons
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (R.B.); (M.C.); (C.D.); (A.M.); (À.M.); (J.B.)
- Correspondence: (Y.P.); (I.A.)
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8
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Karjalainen M, Tossavainen H, Hellman M, Permi P. HACANCOi: a new H α-detected experiment for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:741-752. [PMID: 33118136 PMCID: PMC7701164 DOI: 10.1007/s10858-020-00347-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Unidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the favorable relaxation properties. Long coherence transfer routes now result in prohibitively large decrease in sensitivity. We introduce a novel 4D 1Hα-detected experiment HACANCOi, together with its 3D implementation, which warrant high sensitivity for the assignment of proline-rich regions in IDPs in complex with a globular protein. The experiment correlates 1Hαi, 13Cαi, 15Ni and [Formula: see text] spins by transferring the magnetization concomitantly from 13Cαi to 15Ni and [Formula: see text]. The B1 domain of protein G (GB1), and the enteropathogenic E. coli EspF in complex with human SNX9 SH3, serve as model systems to demonstrate the attainable sensitivity and successful sequential assignment.
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Affiliation(s)
- Mikael Karjalainen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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9
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Abstract
Most cytosolic eukaryotic proteins contain a mixture of ordered and disordered regions. Disordered regions facilitate cell signaling by concentrating sites for posttranslational modifications and protein-protein interactions into arrays of short linear motifs that can be reorganized by RNA splicing. The evolution of disordered regions looks different from their ordered counterparts. In some cases, selection is focused on maintaining protein binding interfaces and PTM sites, but sequence heterogeneity is common. In other cases, simple properties like charge, length, or end-to-end distance are maintained. Many disordered protein binding sites contain some transient secondary structure that may resemble the structure of the bound state. α-Helical secondary structure is common and a wide range of fractional helicity is observed in different disordered regions. Here we provide a simple protocol to identify transient helical segments and design mutants that can change their structure and function.
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10
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Tossavainen H, Salovaara S, Hellman M, Ihalin R, Permi P. Dispersion from C α or N H: 4D experiments for backbone resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:147-159. [PMID: 31932991 PMCID: PMC7080685 DOI: 10.1007/s10858-020-00299-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/02/2020] [Indexed: 05/07/2023]
Abstract
Resonance assignment of intrinsically disordered proteins is remarkably challenging due to scant chemical shift dispersion arising from conformational heterogeneity. The challenge is even greater if repeating segments are present in the amino acid sequence. To forward unambiguous resonance assignment of intrinsically disordered proteins, we present iHACANCO, HACACON and (HACA)CONCAHA, three Hα-detected 4D experiments with Cα as an additional dimension. In addition, we present (HACA)CON(CA)NH and (HACA)N(CA)CONH, new 4D Hα-start, HN-detect experiments which have two NH dimensions to enhance peak dispersion in a sequential walk through C', NH and HN, and provide more accurate NH/HN chemical shifts than those that can be obtained from a crowded 1H, 15N-HSQC spectrum. Application of these 4D experiments is demonstrated using BilRI (165 aa), an outer-membrane intrinsically disordered protein from the opportunistic oral pathogen Aggregatibacter actinomycetemcomitans. BilRI amino acid sequence encompasses three very similar repeats with a 13-residue identical stretch in two of them.
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Affiliation(s)
- Helena Tossavainen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Santeri Salovaara
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Riikka Ihalin
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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11
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Levy R, Gregory E, Borcherds W, Daughdrill G. p53 Phosphomimetics Preserve Transient Secondary Structure but Reduce Binding to Mdm2 and MdmX. Biomolecules 2019; 9:biom9030083. [PMID: 30832340 PMCID: PMC6468375 DOI: 10.3390/biom9030083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The disordered p53 transactivation domain (p53TAD) contains specific levels of transient helical secondary structure that are necessary for its binding to the negative regulators, mouse double minute 2 (Mdm2) and MdmX. The interactions of p53 with Mdm2 and MdmX are also modulated by posttranslational modifications (PTMs) of p53TAD including phosphorylation at S15, T18 and S20 that inhibits p53-Mdm2 binding. It is unclear whether the levels of transient secondary structure in p53TAD are changed by phosphorylation or other PTMs. We used phosphomimetic mutants to determine if adding a negative charge at positions 15 and 18 has any effect on the transient secondary structure of p53TAD and protein-protein binding. Using a combination of biophysical and structural methods, we investigated the effects of single and multisite phosphomimetics on the transient secondary structure of p53TAD and its interaction with Mdm2, MdmX, and the KIX domain. The phosphomimetics reduced Mdm2 and MdmX binding affinity by 3–5-fold, but resulted in minimal changes in transient secondary structure, suggesting that the destabilizing effect of phosphorylation on the p53TAD-Mdm2 interaction is primarily electrostatic. Phosphomimetics had no effect on the p53-KIX interaction, suggesting that increased binding of phosphorylated p53 to KIX may be influenced by decreased competition with its negative regulators.
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Affiliation(s)
- Robin Levy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Emily Gregory
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Wade Borcherds
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
- Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA.
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