1
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Bickel D, Vranken W. Effects of Phosphorylation on Protein Backbone Dynamics and Conformational Preferences. J Chem Theory Comput 2024; 20:4998-5011. [PMID: 38830621 PMCID: PMC11210476 DOI: 10.1021/acs.jctc.4c00206] [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: 02/19/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024]
Abstract
Phosphorylations are the most common and extensively studied post-translational modification (PTM) of proteins in eukaryotes. They constitute a major regulatory mechanism, modulating protein function, protein-protein interactions, as well as subcellular localization. Phosphorylation sites are preferably located in intrinsically disordered regions and have been shown to trigger structural rearrangements and order-to-disorder transitions. They can therefore have a significant effect on protein backbone dynamics or conformation, but only sparse experimental data are available. To obtain a more general description of how and when phosphorylations have a significant effect on protein behavior, molecular dynamics (MD) currently provides the only suitable framework to study these effects at a large scale in atomistic detail. This study develops a systematic MD simulation framework to explore the influence of phosphorylations on the local backbone dynamics and conformational propensities of proteins. Through a series of glycine-backbone peptides, we studied the effects of amino acid residues including the three most common phosphorylations (Ser, Thr, and Tyr), on local backbone dynamics and conformational propensities. We further extended our study to investigate the interactions of all such residues between position i to positions i + 1, i + 2, i + 3, and i + 4 in such peptides. The final data set comprises structural ensembles for 3393 sequences with more than 1 μs of sampling for each ensemble. To validate the relevance of the results, the structural and conformational properties extracted from the MD simulations are compared to NMR data from the Biological Magnetic Resonance Data Bank. The systematic nature of this study enables the projection of the gained knowledge onto any phosphorylation site in the proteome and provides a general framework for the study of further PTMs. The full data set is publicly available, as a training and reference set.
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Affiliation(s)
- David Bickel
- Interuniversity
Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussels, 1050 Brussels, Belgium
| | - Wim Vranken
- Interuniversity
Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussels, 1050 Brussels, Belgium
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2
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Okmane L, Sandgren M, Ståhlberg J, Nestor G. 1H, 13C and 15N backbone resonance assignment of Cel45A from Phanerochaete chrysosporium. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10182-6. [PMID: 38888713 DOI: 10.1007/s12104-024-10182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
A glycoside hydrolase family 45 (GH45) enzyme from the white-rot basidiomycete fungus Phanerochaete chrysosporium (PcCel45A) was expressed in Pichia pastoris with 13C and 15N labelling. A nearly complete assignment of 1H, 13C and 15N backbone resonances was obtained, as well as the secondary structure prediction based on the assigned chemical shifts using the TALOS-N software. The predicted secondary structure was almost identical to previously published crystal structures of the same enzyme, except for differences in the termini of the sequence. This is the first NMR study using an isotopically labelled GH45 enzyme.
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Affiliation(s)
- Laura Okmane
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gustav Nestor
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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3
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Hsu MF, Sriramoju MK, Lai CH, Chen YR, Huang JS, Ko TP, Huang KF, Hsu STD. Structure, dynamics, and stability of the smallest and most complex 7 1 protein knot. J Biol Chem 2024; 300:105553. [PMID: 38072060 PMCID: PMC10840475 DOI: 10.1016/j.jbc.2023.105553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins, but the predictions remain to be authenticated experimentally. Here, we showed by X-ray crystallography and solution-state NMR spectroscopy that Q9PR55, an 89-residue protein from Ureaplasma urealyticum, possesses a novel 71 knotted topology that is accurately predicted by AlphaFold 2, except for the flexible N terminus. Q9PR55 is monomeric in solution, making it the smallest and most complex knotted protein known to date. In addition to its exceptional chemical stability against urea-induced unfolding, Q9PR55 is remarkably robust to resist the mechanical unfolding-coupled proteolysis by a bacterial proteasome, ClpXP. Our results suggest that the mechanical resistance against pulling-induced unfolding is determined by the complexity of the knotted topology rather than the size of the molecule.
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Affiliation(s)
- Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Jing-Siou Huang
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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4
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Shukla VK, Heller GT, Hansen DF. Biomolecular NMR spectroscopy in the era of artificial intelligence. Structure 2023; 31:1360-1374. [PMID: 37848030 DOI: 10.1016/j.str.2023.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in accurately characterizing protein dynamics, allostery, and conformational heterogeneity. We begin by highlighting the unique abilities of biomolecular NMR spectroscopy to complement AI-based structural predictions toward addressing these knowledge gaps. We then highlight the direct integration of deep learning approaches into biomolecular NMR methods. AI-based tools can dramatically improve the acquisition and analysis of NMR spectra, enhancing the accuracy and reliability of NMR measurements, thus streamlining experimental processes. Additionally, deep learning enables the development of novel types of NMR experiments that were previously unattainable, expanding the scope and potential of biomolecular NMR spectroscopy. Ultimately, a combination of AI and NMR promises to further revolutionize structural biology on several levels, advance our understanding of complex biomolecular systems, and accelerate drug discovery efforts.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Gabriella T Heller
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
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5
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Peck Y, Pickering D, Mobli M, Liddell MJ, Wilson DT, Ruscher R, Ryan S, Buitrago G, McHugh C, Love NC, Pinlac T, Haertlein M, Kron MA, Loukas A, Daly NL. Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase. J Biomol Struct Dyn 2023:1-11. [PMID: 37572327 DOI: 10.1080/07391102.2023.2241918] [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: 01/11/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Several secreted proteins from helminths (parasitic worms) have been shown to have immunomodulatory activities. Asparaginyl-tRNA synthetases are abundantly secreted in the filarial nematode Brugia malayi (BmAsnRS) and the parasitic flatworm Schistosoma japonicum (SjAsnRS), indicating a possible immune function. The suggestion is supported by BmAsnRS alleviating disease symptoms in a T-cell transfer mouse model of colitis. This immunomodulatory function is potentially related to an N-terminal extension domain present in eukaryotic AsnRS proteins but few structure/function studies have been done on this domain. Here we have determined the three-dimensional solution structure of the N-terminal extension domain of SjAsnRS. A protein containing the 114 N-terminal amino acids of SjAsnRS was recombinantly expressed with isotopic labelling to allow structure determination using 3D NMR spectroscopy, and analysis of dynamics using NMR relaxation experiments. Structural comparisons of the N-terminal extension domain of SjAsnRS with filarial and human homologues highlight a high degree of variability in the β-hairpin region of these eukaryotic N-AsnRS proteins, but similarities in the disorder of the C-terminal regions. Limitations in PrDOS-based intrinsically disordered region (IDR) model predictions were also evident in this comparison. Empirical structural data such as that presented in our study for N-SjAsnRS will enhance the prediction of sequence-homology based structure modelling and prediction of IDRs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yoshimi Peck
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren Pickering
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Michael J Liddell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Stephanie Ryan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Geraldine Buitrago
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Connor McHugh
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | | | - Theresa Pinlac
- Department of Biochemistry, University of the Philippines, Manila, Philippines
| | | | - Michael A Kron
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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6
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Fowler NJ, Albalwi MF, Lee S, Hounslow AM, Williamson MP. Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1. Structure 2023; 31:975-986.e3. [PMID: 37311460 DOI: 10.1016/j.str.2023.05.012] [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: 03/10/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
Protein structures calculated using NMR data are less accurate and less well-defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
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Affiliation(s)
- Nicholas J Fowler
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
| | - Marym F Albalwi
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Subin Lee
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Andrea M Hounslow
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK.
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7
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Arianna GA, Geddes-Buehre DH, Korzhnev DM. Backbone and ILV side-chain methyl NMR resonance assignments of human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes. BIOMOLECULAR NMR ASSIGNMENTS 2023:10.1007/s12104-023-10128-4. [PMID: 37129702 DOI: 10.1007/s12104-023-10128-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Rev7 is a versatile HORMA (Hop1, Rev7, Mad2) family adaptor protein with multiple roles in mitotic regulation and DNA damage response, and an essential accessory subunit of the translesion synthesis (TLS) DNA polymerase Polζ employed in replication of damaged DNA. Within Polζ, the two copies of Rev7 interact with the two Rev7-bonding motifs (RBM1 and RBM2) of the catalytic subunit Rev3 by a mechanism characteristic of HORMA proteins whereby the "safety-belt" loop of Rev7 closes on the top of the ligand. Here we report the nearly complete backbone and Ile, Val, Leu side-chain methyl NMR resonance assignments of the 27 kDa human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes (BMRB deposition numbers 51651 and 51652) that will facilitate future NMR studies of Rev7 dynamics and interactions.
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Affiliation(s)
- Gianluca A Arianna
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Dane H Geddes-Buehre
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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8
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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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9
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Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:biom12091246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand binding, including allosteric effects, protein–protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
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10
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The accuracy of protein structures in solution determined by AlphaFold and NMR. Structure 2022; 30:925-933.e2. [DOI: 10.1016/j.str.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 02/05/2023]
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11
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Malär AA, Callon M, Smith AA, Wang S, Lecoq L, Pérez-Segura C, Hadden-Perilla JA, Böckmann A, Meier BH. Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR. Front Mol Biosci 2022; 8:807577. [PMID: 35047563 PMCID: PMC8762115 DOI: 10.3389/fmolb.2021.807577] [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] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
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Affiliation(s)
| | | | - Albert A Smith
- Institute of Medical Physics and Biophysics, Universität Leipzig, Leipzig, Germany
| | - Shishan Wang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
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12
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Rehman MF, Jeeves M, Hyde EI. Backbone assignments, and effect of Asn deamidation, of the N-terminal region of the partitioning protein IncC1 from the plasmid RK2. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:305-310. [PMID: 33856628 PMCID: PMC8481139 DOI: 10.1007/s12104-021-10021-y] [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: 02/08/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
IncC from the low-copy number plasmid RK2, is a member of the ParA family of proteins required for partitioning DNA in many bacteria and plasmids. It is an ATPase that binds DNA and its ParB protein partner, KorB. Together, the proteins move replicated DNA to appropriate cellular positions, so that each daughter cell inherits a copy on cell division. IncC from RK2 is expressed in two forms. IncC2 is homologous to bacterial ParA proteins, while IncC1 has an N-terminal extension of 105 amino acids and is similar in length to ParA homologues in other plasmids. We have been examining the role of this extension, here called IncC NTD. We present its backbone NMR chemical shift assignments and show that it is entirely intrinsically disordered. The assignments were achieved using C-detected, CON-based spectra, complemented by HNN spectra to obtain connectivities from three adjacent amino acids. We also observed evidence of deamidation of the protein at a GNGG sequence, to give isoAsp, giving 2 sets of peaks for residues up to 5 amino acids on either side of the modification. We have assigned resonances from around the position of modification for this form of the protein.
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Affiliation(s)
- M Fayyaz Rehman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Chemistry, University of Sargodha, Sargodha, Punjab, Pakistan
| | - M Jeeves
- Henry Wellcome NMR Centre, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - E I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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13
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Mahdi S, Bezsonova I, Beuning PJ, Korzhnev DM. NMR resonance assignments for the nucleotide binding domains of the E. coli clamp loader complex γ subunit. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:281-285. [PMID: 33761093 PMCID: PMC8460709 DOI: 10.1007/s12104-021-10018-7] [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: 02/10/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
The E. coli γ clamp loader is a pentameric complex of δ, δ' and three γ subunits that opens and loads β-clamp proteins onto DNA in an ATP-dependent process essential for efficient DNA replication. ATP binding to the γ subunits promotes conformational changes that enable the clamp loader to bind and open the ring-shaped β-clamp homodimer. Here we report the nearly complete backbone and side-chain 1H, 13C and 15N NMR resonance assignments of the 242-residue truncated γ subunit of the clamp loader complex, which includes the N-terminal mini (domain I) and lid (domain II) domains. This construct represents the nucleotide binding module in the clamp loader complex and provides a model system for studies of conformational rearrangements of the clamp loader induced by nucleotide binding.
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Affiliation(s)
- Sam Mahdi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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14
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Labrecque CL, Fuglestad B. Electrostatic Drivers of GPx4 Interactions with Membrane, Lipids, and DNA. Biochemistry 2021; 60:2761-2772. [PMID: 34492183 DOI: 10.1021/acs.biochem.1c00492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Glutathione peroxidase 4 (GPx4) serves as the only enzyme that protects membranes through the reduction of lipid hydroperoxides, preventing membrane oxidative damage and cell death through ferroptosis. Recently, GPx4 has gained attention as a therapeutic target for cancer through inhibition and as a target for inflammatory diseases through activation. In addition, GPx4 isoforms perform several distinct moonlighting functions including cysteine cross-linking of protamines during sperm cell chromatin remodeling, a function for which molecular and structural details are undefined. Despite the importance in biology, disease, and potential for drug development, little is known about GPx4 functional interactions at high resolution. This study presents the first NMR assignments of GPx4, and the electrostatic interaction of GPx4 with the membrane is characterized. Mutagenesis reveals the cationic patch residues that are key to membrane binding and stabilization. The cationic patch is observed to be important in binding headgroups of highly anionic cardiolipin. A novel lipid binding site is observed adjacent to the catalytic site and may enable protection of lipid-headgroups from oxidative damage. Arachidonic acid is also found to engage with GPx4, while cholesterol did not display any interaction. The cationic patch residues were also found to enable DNA binding, the first observation of this interaction. Electrostatic DNA binding explains a mechanism for the nuclear isoform of GPx4 to target DNA-bound protamines and to potentially reduce oxidatively damaged DNA. Together, these results highlight the importance of electrostatics in the function of GPx4 and illuminate how the multifunctional enzyme is able to fill multiple biological roles.
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Affiliation(s)
- Courtney L Labrecque
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States.,Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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15
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Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure 2021; 29:1430-1439.e2. [PMID: 34331857 DOI: 10.1016/j.str.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a need for more experimental restraints in loops. Currently, the best predictors of accuracy are Ramachandran distribution and the number of NOE restraints per residue. The precision of structures within the ensemble correlates well with accuracy, as does the number of hydrogen bond restraints per residue. Structure accuracy is improved when other components (such as additional polypeptide chains or ligands) are included.
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Affiliation(s)
- Nicholas J Fowler
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027 Japan; Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada.
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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16
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Kumar SU, Priya Doss CG. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop. Comput Biol Med 2021; 135:104597. [PMID: 34237589 DOI: 10.1016/j.compbiomed.2021.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
Abstract
The mutant K-Ras with aberrant signaling is the primary cause of several cancers. The proposed study investigated the influence of water molecules in K-Ras crystal structure, where they have a significant function by understanding their residue interaction networks (RINs). We analyzed the RINs of K-Ras with and without water molecules and determined their interaction properties. RINs were developed with the help of StructureViz2 and RINspector; further, the changes in K-Ras backbone flexibility were predicted with the DynaMine. We found that the residues K42, I142, and L159 are the hotspots from water, including the K-Ras-GTP complex with the highest residue centrality analysis (RCA) Z-score. The DynaMine prediction calculated the NMR S2 value for the frequently mutated positions G12, G13, and Q61 showing a minor shift in flexibility, which make up the P-Loop and switch II of the K-Ras protein. This flexibility shift can account for changes in conformational activity and the protein's GTPase activity, making it difficult to recognize by the effectors and exchange factors. Taken together, our study helps in understanding the functional importance of the water molecules in K-Ras protein and the impact of mutation that modulate the conformational state of the protein.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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17
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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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18
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Zhou T, Fleming JR, Lange S, Hessel AL, Bogomolovas J, Stronczek C, Grundei D, Ghassemian M, Biju A, Börgeson E, Bullard B, Linke WA, Chen J, Kovermann M, Mayans O. Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism. J Mol Biol 2021; 433:166901. [PMID: 33647290 PMCID: PMC8052292 DOI: 10.1016/j.jmb.2021.166901] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
Striated muscle responds to mechanical overload by rapidly up-regulating the expression of the cardiac ankyrin repeat protein, CARP, which then targets the sarcomere by binding to titin N2A in the I-band region. To date, the role of this interaction in the stress response of muscle remains poorly understood. Here, we characterise the molecular structure of the CARP-receptor site in titin (UN2A) and its binding of CARP. We find that titin UN2A contains a central three-helix bundle fold (ca 45 residues in length) that is joined to N- and C-terminal flanking immunoglobulin domains by long, flexible linkers with partial helical content. CARP binds titin by engaging an α-hairpin in the three-helix fold of UN2A, the C-terminal linker sequence, and the BC loop in Ig81, which jointly form a broad binding interface. Mutagenesis showed that the CARP/N2A association withstands sequence variations in titin N2A and we use this information to evaluate 85 human single nucleotide variants. In addition, actin co-sedimentation, co-transfection in C2C12 cells, proteomics on heart lysates, and the mechanical response of CARP-soaked myofibrils imply that CARP induces the cross-linking of titin and actin myofilaments, thereby increasing myofibril stiffness. We conclude that CARP acts as a regulator of force output in the sarcomere that preserves muscle mechanical performance upon overload stress.
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Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Stephan Lange
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Anthony L Hessel
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Julius Bogomolovas
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Chiara Stronczek
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David Grundei
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry, University of California, San Diego 92093, CA, USA
| | - Andrea Biju
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA
| | - Emma Börgeson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Wolfgang A Linke
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Ju Chen
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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19
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Hyde EI, Chau AKW, Smith LJ. Backbone assignment of E. coli NfsB and the effects of addition of the cofactor analogue nicotinic acid. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:143-151. [PMID: 33423170 PMCID: PMC7974150 DOI: 10.1007/s12104-020-09997-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
E. coli nitroreductase NfsB (also called NfnB) has been studied extensively, largely due to its potential for cancer gene therapy. A homodimeric flavoprotein of 216 residues, it catalyses the reduction of nitroaromatics to cytotoxic hydroxylamines by NADH and NADPH and also the reduction of quinones to hydroxyquinones. Its role in vivo is not known but it is postulated to be involved in reducing oxidative stress. The crystal structures of the wild type protein and several homologues have been determined in the absence and presence of ligands, including nicotinate as a mimic of the headpiece of the nicotinamide cofactors. There is little effect on the overall structure of the protein on binding ligands, but, from the B factors, there appears to be a decrease in mobility of 2 helices near the active site. As a first step towards examining the dynamics of the protein in solution with and without ligand, we have assigned the backbone 13C, 15N, and 1HN resonances of NfsB and examined the effect of the binding of nicotinate on the amide 15N, and 1HN shifts.
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Affiliation(s)
- Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Alex Ka-Wing Chau
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Legislative Council Complex, Central, Hong Kong
| | - Lorna J Smith
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK.
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20
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Mapping temperature-dependent conformational change in the voltage-sensing domain of an engineered heat-activated K + channel. Proc Natl Acad Sci U S A 2021; 118:2017280118. [PMID: 33782120 DOI: 10.1073/pnas.2017280118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Temperature-dependent regulation of ion channel activity is critical for a variety of physiological processes ranging from immune response to perception of noxious stimuli. Our understanding of the structural mechanisms that underlie temperature sensing remains limited, in part due to the difficulty of combining high-resolution structural analysis with temperature stimulus. Here, we use NMR to compare the temperature-dependent behavior of Shaker potassium channel voltage sensor domain (WT-VSD) to its engineered temperature sensitive (TS-VSD) variant. Further insight into the molecular basis for temperature-dependent behavior is obtained by analyzing the experimental results together with molecular dynamics simulations. Our studies reveal that the overall secondary structure of the engineered TS-VSD is identical to the wild-type channels except for local changes in backbone torsion angles near the site of substitution (V369S and F370S). Remarkably however, these structural differences result in increased hydration of the voltage-sensing arginines and the S4-S5 linker helix in the TS-VSD at higher temperatures, in contrast to the WT-VSD. These findings highlight how subtle differences in the primary structure can result in large-scale changes in solvation and thereby confer increased temperature-dependent activity beyond that predicted by linear summation of solvation energies of individual substituents.
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21
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Czajlik A, Holzknecht J, Galgóczy L, Tóth L, Poór P, Ördög A, Váradi G, Kühbacher A, Borics A, Tóth GK, Marx F, Batta G. Solution Structure, Dynamics, and New Antifungal Aspects of the Cysteine-Rich Miniprotein PAFC. Int J Mol Sci 2021; 22:1183. [PMID: 33504082 PMCID: PMC7865535 DOI: 10.3390/ijms22031183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The genome of Penicillium chrysogenum Q176 contains a gene coding for the 88-amino-acid (aa)-long glycine- and cysteine-rich P. chrysogenum antifungal protein C (PAFC). After maturation, the secreted antifungal miniprotein (MP) comprises 64 aa and shares 80% aa identity with the bubble protein (BP) from Penicillium brevicompactum, which has a published X-ray structure. Our team expressed isotope (15N, 13C)-labeled, recombinant PAFC in high yields, which allowed us to determine the solution structure and molecular dynamics by nuclear magnetic resonance (NMR) experiments. The primary structure of PAFC is dominated by 14 glycines, and therefore, whether the four disulfide bonds can stabilize the fold is challenging. Indeed, unlike the few published solution structures of other antifungal MPs from filamentous ascomycetes, the NMR data indicate that PAFC has shorter secondary structure elements and lacks the typical β-barrel structure, though it has a positively charged cavity and a hydrophobic core around the disulfide bonds. Some parts within the two putative γ-core motifs exhibited enhanced dynamics according to a new disorder index presentation of 15N-NMR relaxation data. Furthermore, we also provided a more detailed insight into the antifungal spectrum of PAFC, with specific emphasis on fungal plant pathogens. Our results suggest that PAFC could be an effective candidate for the development of new antifungal strategies in agriculture.
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Affiliation(s)
- András Czajlik
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Jeanett Holzknecht
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (J.H.); (A.K.)
| | - László Galgóczy
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (L.G.); (L.T.)
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Liliána Tóth
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (L.G.); (L.T.)
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Péter Poór
- Department of Plant Biology, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary; (P.P.); (A.Ö.)
| | - Attila Ördög
- Department of Plant Biology, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary; (P.P.); (A.Ö.)
| | - Györgyi Váradi
- Department of Medical Chemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (G.V.); (G.K.T.)
| | - Alexander Kühbacher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (J.H.); (A.K.)
| | - Attila Borics
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary;
| | - Gábor K. Tóth
- Department of Medical Chemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (G.V.); (G.K.T.)
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Florentine Marx
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (J.H.); (A.K.)
| | - Gyula Batta
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary;
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22
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Fowler NJ, Sljoka A, Williamson MP. A method for validating the accuracy of NMR protein structures. Nat Commun 2020; 11:6321. [PMID: 33339822 PMCID: PMC7749147 DOI: 10.1038/s41467-020-20177-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/13/2020] [Indexed: 01/13/2023] Open
Abstract
We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.
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Affiliation(s)
- Nicholas J Fowler
- Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Dept of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada.
| | - Mike P Williamson
- Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
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23
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Abdulganiyyu IA, Kaczmarek K, Zabrocki J, Nachman RJ, Marchal E, Schellens S, Verlinden H, Broeck JV, Marco H, Jackson GE. Conformational analysis of a cyclic AKH neuropeptide analog that elicits selective activity on locust versus honeybee receptor. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 125:103362. [PMID: 32730893 DOI: 10.1016/j.ibmb.2020.103362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/02/2020] [Accepted: 03/15/2020] [Indexed: 06/11/2023]
Abstract
Neuropeptides belonging to the adipokinetic hormone (AKH) family elicit metabolic effects as their main function in insects, by mobilizing trehalose, diacylgycerol, or proline, which are released from the fat body into the hemolymph as energy sources for muscle contraction required for energy-intensive processes, such as locomotion. One of the AKHs produced in locusts is a decapeptide, Locmi-AKH-I (pELNFTPNWGT-NH2). A head-to-tail cyclic, octapeptide analog of Locmi-AKH-I, cycloAKH (cyclo[LNFTPNWG]) was synthesized to severely restrict the conformational freedom of the AKH structure. In vitro, cycloAKH selectively retains full efficacy on a pest insect (desert locust) AKH receptor, while showing little or no activation of the AKH receptor of a beneficial insect (honeybee). Molecular dynamic analysis incorporating NMR data indicate that cycloAKH preferentially adopts a type II β-turn under micelle conditions, whereas its linear counterpart and natural AKH adopts a type VI β-turn under similar conditions. CycloAKH, linear LNFTPNWG-NH2, and Locmi-AKH-I feature the same binding site during docking simulations with the desert locust AKH receptor (Schgr-AKHR), but differ in the details of the ligand/receptor interactions. However, cycloAKH failed to enter the binding pocket of the honeybee receptor 3D model during docking simulations. Since the locust AKH receptor has a greater tolerance than the honeybee receptor for the cyclic conformational constraint in vitro receptor assays, it could suggest a greater tolerance for a shift in the direction of the type II β turn exhibited by cycloAKH from the type VI β turn of the linear octapeptide and the native locust decapeptide AKH. Selectivity in biostable mimetic analogs could potentially be enhanced by incorporating conformational constraints that emphasize this shift. Biostable mimetic analogs of AKH offer the potential of selectively disrupting AKH-regulated processes, leading to novel, environmentally benign control strategies for pest insect populations.
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Affiliation(s)
- Ibrahim A Abdulganiyyu
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Krzysztof Kaczmarek
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, U.S. Department of Agriculture, 2881 F/B Road, College Station, TX 77845, USA; Lodz University of Technology, 90-924, Lodz, Poland
| | - Janusz Zabrocki
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, U.S. Department of Agriculture, 2881 F/B Road, College Station, TX 77845, USA; Lodz University of Technology, 90-924, Lodz, Poland
| | - Ronald J Nachman
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, U.S. Department of Agriculture, 2881 F/B Road, College Station, TX 77845, USA.
| | - Elisabeth Marchal
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Sam Schellens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Heleen Verlinden
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Heather Marco
- Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
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24
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Tolkatchev D, Smith GE, Schultz LE, Colpan M, Helms GL, Cort JR, Gregorio CC, Kostyukova AS. Leiomodin creates a leaky cap at the pointed end of actin-thin filaments. PLoS Biol 2020; 18:e3000848. [PMID: 32898131 PMCID: PMC7500696 DOI: 10.1371/journal.pbio.3000848] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/18/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023] Open
Abstract
Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a "swinging gate" allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.
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Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Garry E. Smith
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Lauren E. Schultz
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Mert Colpan
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Gregory L. Helms
- The Center for NMR Spectroscopy, Washington State University, Pullman, Washington, United States of America
| | - John R. Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
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25
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Danielsson J, Noel JK, Simien JM, Duggan BM, Oliveberg M, Onuchic JN, Jennings PA, Haglund E. The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III. J Mol Biol 2020; 432:3050-3063. [PMID: 32081588 DOI: 10.1016/j.jmb.2020.01.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/18/2020] [Accepted: 01/24/2020] [Indexed: 02/08/2023]
Abstract
Leptin is an important signaling hormone, mostly known for its role in energy expenditure and satiety. Furthermore, leptin plays a major role in other proteinopathies, such as cancer, marked hyperphagia, impaired immune function, and inflammation. In spite of its biological relevance in human health, there are no NMR resonance assignments of the human protein available, obscuring high-resolution characterization of the soluble protein and/or its conformational dynamics, suggested as being important for receptor interaction and biological activity. Here, we report the nearly complete backbone resonance assignments of human leptin. Chemical shift-based secondary structure prediction confirms that in solution leptin forms a four-helix bundle including a pierced lasso topology. The conformational dynamics, determined on several timescales, show that leptin is monomeric, has a rigid four-helix scaffold, and a dynamic domain, including a transiently formed helix. The dynamic domain is anchored to the helical scaffold by a secondary hydrophobic core, pinning down the long loops of leptin to the protein body, inducing motional restriction without a well-defined secondary or tertiary hydrogen bond stabilized structure. This dynamic region is well suited for and may be involved in functional allosteric dynamics upon receptor binding.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | | | | | - Brendan Michael Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, USA
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, USA; Department of Physics and Astronomy, Department of Chemistry, And Department of Biosciences, Rice University, Houston, USA
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, The University of California at San Diego, La Jolla, USA
| | - Ellinor Haglund
- The Department of Chemistry, University of Hawaii, Manoa, Honolulu, USA.
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26
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Xhani S, Lee S, Kim HM, Wang S, Esaki S, Ha VLT, Khanezarrin M, Fernandez GL, Albrecht AV, Aramini JM, Germann MW, Poon GMK. Intrinsic disorder controls two functionally distinct dimers of the master transcription factor PU.1. SCIENCE ADVANCES 2020; 6:eaay3178. [PMID: 32128405 PMCID: PMC7034988 DOI: 10.1126/sciadv.aay3178] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/04/2019] [Indexed: 06/01/2023]
Abstract
Transcription factors comprise a major reservoir of conformational disorder in the eukaryotic proteome. The hematopoietic master regulator PU.1 presents a well-defined model of the most common configuration of intrinsically disordered regions (IDRs) in transcription factors. We report that the structured DNA binding domain (DBD) of PU.1 regulates gene expression via antagonistic dimeric states that are reciprocally controlled by cognate DNA on the one hand and by its proximal anionic IDR on the other. The two conformers are mediated by distinct regions of the DBD without structured contributions from the tethered IDRs. Unlike DNA-bound complexes, the unbound dimer is markedly destabilized. Dimerization without DNA is promoted by progressive phosphomimetic substitutions of IDR residues that are phosphorylated in immune activation and stimulated by anionic crowding agents. These results suggest a previously unidentified, nonstructural role for charged IDRs in conformational control by mitigating electrostatic penalties that would mask the interactions of highly cationic DBDs.
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Affiliation(s)
- Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Sangchoon Lee
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Shingo Esaki
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Van L. T. Ha
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Mahtab Khanezarrin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | | | - Amanda V. Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - James M. Aramini
- Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Gregory M. K. Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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27
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Rodriguez G, Orris B, Majumdar A, Bhat S, Stivers JT. Macromolecular crowding induces compaction and DNA binding in the disordered N-terminal domain of hUNG2. DNA Repair (Amst) 2019; 86:102764. [PMID: 31855846 DOI: 10.1016/j.dnarep.2019.102764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 11/15/2022]
Abstract
Many human DNA repair proteins have disordered domains at their N- or C-termini with poorly defined biological functions. We recently reported that the partially structured N-terminal domain (NTD) of human uracil DNA glycosylase 2 (hUNG2), functions to enhance DNA translocation in crowded environments and also targets the enzyme to single-stranded/double-stranded DNA junctions. To understand the structural basis for these effects we now report high-resolution heteronuclear NMR studies of the isolated NTD in the presence and absence of an inert macromolecular crowding agent (PEG8K). Compared to dilute buffer, we find that crowding reduces the degrees of freedom for the structural ensemble, increases the order of a PCNA binding motif and dramatically promotes binding of the NTD for DNA through a conformational selection mechanism. These findings shed new light on the function of this disordered domain in the context of the crowded nuclear environment.
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Affiliation(s)
- Gaddiel Rodriguez
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States
| | - Benjamin Orris
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States.
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28
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Scorciapino MA, Carta P, Pantic J, Lukic ML, Lukic A, Musale V, Abdel-Wahab YHA, Conlon JM. Conformational analysis and in vitro immunomodulatory and insulinotropic properties of the frog skin host-defense peptide rhinophrynin-27 and selected analogs. Biochimie 2019; 167:198-206. [PMID: 31639404 DOI: 10.1016/j.biochi.2019.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/16/2019] [Indexed: 02/09/2023]
Abstract
The study investigates conformational analysis and the in vitro cytokine-mediated immunomodulatory and insulin-releasing activities of rhinophrynin-27 (ELRLPEIARPVPEVLPARLPLPALPRN; RP-27), a proline-arginine-rich peptide first isolated from skin secretions of the Mexican burrowing toad Rhinophrynus dorsalis (Rhinophrynidae). In both water and 50% trifluoroethanol-water, the peptide adopts a polyproline type II helical conformation with a high degree of deviation from the canonical collagen-like folding and a pronounced bend in the molecule at the Glu13 residue. Incubation of mouse peritoneal cells with RP-27 significantly (P < 0.05) inhibited production of the pro-inflammatory cytokines TNF-α and IL-1β and stimulated production of the anti-inflammatory cytokine IL-10. The peptide significantly (P < 0.01) stimulated release of insulin from BRIN-BD11 rat clonal β-cells at concentrations ≥ 1 nM while maintaining the integrity of the plasma membrane and also stimulated insulin release from isolated mouse islets at a concentration of 10-6 M. Increasing the cationicity of RP-27 by substituting glutamic acid residues in the peptide by arginine and increasing hydrophobicity by substituting alanine residues by tryptophan did not result in analogues with increased activity with respect to cytokine production and insulin release. The combination of immunosuppressive and insulinotropic activities together with very low cytotoxicity suggests that RP-27 may represent a template for the development of an agent for use in anti-inflammatory and Type 2 diabetes therapies.
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Affiliation(s)
- Mariano A Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Italy
| | - Paola Carta
- Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Italy
| | - Jelena Pantic
- Center for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Miodrag L Lukic
- Department of Endodontics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Aleksandra Lukic
- Department of Endodontics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Vishal Musale
- Diabetes Research Group, School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, N. Ireland, UK
| | - Yasser H A Abdel-Wahab
- Diabetes Research Group, School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, N. Ireland, UK
| | - J Michael Conlon
- Diabetes Research Group, School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, N. Ireland, UK.
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29
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Farina B, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Isernia C, Saviano M, Fattorusso R, Zaccaro L, Russo L. Conformational studies of RGDechi peptide by natural-abundance NMR spectroscopy. J Pept Sci 2019; 25:e3166. [PMID: 30884005 DOI: 10.1002/psc.3166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/24/2022]
Abstract
Integrins are heterodimeric cell-surface proteins that play important roles during developmental and pathological processes. Diverse human pathologies involve integrin adhesion including thrombotic diseases, inflammation, tumour progression, fibrosis, and infectious diseases. Although in the past decade, novel integrin-inhibitor drugs have been developed for integrin-based medical applications, the structural determinants modulating integrin-ligands recognition mechanisms are still poorly understood, reducing the number of integrin subtype exclusive antagonists. In this scenario, we have very recently showed, by means of chemical and biological assays, that a chimeric peptide (named RGDechi), containing a cyclic RGD motif linked to an echistatin C-terminal fragment, is able to interact with the components of integrin family with variable affinities, the highest for αv β3. Here, in order to understand the mechanistic details driving the molecular recognition mechanism of αv β3 by RGDechi, we have performed a detailed structural and dynamics characterization of the free peptide by natural abundance nuclear magnetic resonance (NMR) spectroscopy. Our data indicate that RGDechi presents in solution an heterogeneous conformational ensemble characterized by a more constrained and rigid pentacyclic ring and a largely unstructured acyclic region. Moreover, we propose that the molecular recognition of αv β3 integrin by RGDechi occurs by a combination of conformational selection and induced fit mechanisms. Finally, our study indicates that a detailed NMR characterization, by means of natural abundance 15 N and 13 C, of a mostly unstructured bioactive peptide may provide the molecular basis to get essential structural insights into the binding mechanism to the biological partner.
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Affiliation(s)
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Daniela Comegna
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Domenica Capasso
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | | | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
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30
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Rangarajan S, He Y, Chen Y, Kerzic MC, Ma B, Gowthaman R, Pierce BG, Nussinov R, Mariuzza RA, Orban J. Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. J Biol Chem 2018; 293:15991-16005. [PMID: 30135211 PMCID: PMC6187629 DOI: 10.1074/jbc.ra118.003832] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/21/2018] [Indexed: 12/17/2022] Open
Abstract
T cells generate adaptive immune responses mediated by the T cell receptor (TCR)-CD3 complex comprising an αβ TCR heterodimer noncovalently associated with three CD3 dimers. In early T cell activation, αβ TCR engagement by peptide-major histocompatibility complex (pMHC) is first communicated to the CD3 signaling apparatus of the TCR-CD3 complex, but the underlying mechanism is incompletely understood. It is possible that pMHC binding induces allosteric changes in TCR conformation or dynamics that are then relayed to CD3. Here, we carried out NMR analysis and molecular dynamics (MD) simulations of both the α and β chains of a human antiviral TCR (A6) that recognizes the Tax antigen from human T cell lymphotropic virus-1 bound to the MHC class I molecule HLA-A2. We observed pMHC-induced NMR signal perturbations in the TCR variable (V) domains that propagated to three distinct sites in the constant (C) domains: 1) the Cβ FG loop projecting from the Vβ/Cβ interface; 2) a cluster of Cβ residues near the Cβ αA helix, a region involved in interactions with CD3; and 3) the Cα AB loop at the membrane-proximal base of the TCR. A biological role for each of these allosteric sites is supported by previous mutational and functional studies of TCR signaling. Moreover, the pattern of long-range, ligand-induced changes in TCR A6 revealed by NMR was broadly similar to that predicted by the MD simulations. We propose that the unique structure of the TCR β chain enables allosteric communication between the TCR-binding sites for pMHC and CD3.
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MESH Headings
- Allosteric Regulation
- Animals
- Binding Sites
- Gene Products, tax/chemistry
- Gene Products, tax/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/metabolism
- Human T-lymphotropic virus 1/chemistry
- Humans
- Mice
- Molecular Dynamics Simulation
- Protein Binding
- Protein Conformation
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
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Affiliation(s)
- Sneha Rangarajan
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
- the Departments of Cell Biology and Molecular Genetics and
| | - Yanan He
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
- Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and
| | - Yihong Chen
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Melissa C Kerzic
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
| | - Buyong Ma
- the Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Ragul Gowthaman
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
- the Departments of Cell Biology and Molecular Genetics and
| | - Brian G Pierce
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850
- the Departments of Cell Biology and Molecular Genetics and
| | - Ruth Nussinov
- the Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Roy A Mariuzza
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850,
- the Departments of Cell Biology and Molecular Genetics and
| | - John Orban
- From the W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850,
- Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and
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31
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Manzo G, Serra I, Magrí A, Casu M, De Pinto V, Ceccarelli M, Scorciapino MA. Folded Structure and Membrane Affinity of the N-Terminal Domain of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion-Selective Channel. ACS OMEGA 2018; 3:11415-11425. [PMID: 30320261 PMCID: PMC6173511 DOI: 10.1021/acsomega.8b01536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Voltage-dependent anion-selective channels (VDACs) are primarily located in the mitochondrial outer membrane (MOM). They are essential for the regulation of ion and metabolite exchanges. In particular, their role in energy-related nucleotide exchange has many implications in apoptosis, cancer, and neurodegenerative diseases. It has been proposed that VDACs' functions are regulated by mobility of the N-terminal helical domain, which is bound to the inner wall of the main β-barrel domain but exists in equilibrium between the bound-folded and the unbound-unfolded state. When the N-terminal domain detaches from the channel's wall and eventually leaves the lumen, it can either stay exposed to the cytosolic environment or interact with the outer leaflet of the MOM; then, it may also interact with other protein partners. In humans, three different VDAC isoforms are expressed at different tissue-specific levels with evidence of distinct roles. Although the N-terminal domains share high sequence similarity, important differences do exist, with the functionality of the entire protein mostly attributed to them. In this work, the three-dimensional structure and membrane affinity of the three isolated hVDAC N-terminal peptides have been compared through Fourier-transform infrared and NMR spectroscopy in combination with molecular dynamics simulations, and measurement of the surface pressure of lipid monolayers. Although peptides were studied as isolated from the β-barrel domain, the observed differences are relevant for those whole protein's functions in which a protein-protein interaction is mediated by the N-terminal domain.
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Affiliation(s)
- Giorgia Manzo
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Ilaria Serra
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Andrea Magrí
- Department of Biomedicine
and Biotechnology, Section of Biology and Genetics, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Mariano Casu
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Vito De Pinto
- Department of Biomedicine
and Biotechnology, Section of Biology and Genetics, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Matteo Ceccarelli
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Mariano Andrea Scorciapino
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
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32
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Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:43-58. [DOI: 10.1007/978-981-13-2200-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Alyami EM, Rizzo AA, Beuning PJ, Korzhnev DM. NMR resonance assignments for the N-terminal domain of the δ subunit of the E. coli γ clamp loader complex. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:169-173. [PMID: 28265855 DOI: 10.1007/s12104-017-9741-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
The β-clamp protein and the γ clamp loader complex are essential components of bacterial DNA replication machinery. The β-clamp is a ring-shaped homodimer that encircles DNA and increases the efficiency of replication by providing a binding platform for DNA polymerases and other replication-related proteins. The β-clamp is loaded onto DNA by the five-subunit γ clamp loader complex in a multi-step ATP-dependent process. The initial steps of this process involve the cooperative binding of the β-clamp by the five subunits of ATP-bound clamp loader, which induces or traps an open conformation of the clamp. Remarkably, the δ subunit of the E. coli clamp loader, or even its 140 residue N-terminal domain (called mini-δ), alone can shift conformational equilibrium of the β-clamp towards the open state. Here we report nearly complete backbone and side-chain 1H, 13C and 15N NMR resonance assignments of mini-δ that will facilitate NMR studies of the mechanisms of β-clamp opening and its loading on DNA by the clamp loader.
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Affiliation(s)
- Esmael M Alyami
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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34
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Banerjee A, Ray S. Novel insight into mutational impacts and binding mechanism of human glutaminase and glutaminase-interacting protein: A bio-molecular modeling and docking analysis. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Dubovskii PV, Dubinnyi MA, Konshina AG, Kazakova ED, Sorokoumova GM, Ilyasova TM, Shulepko MA, Chertkova RV, Lyukmanova EN, Dolgikh DA, Arseniev AS, Efremov RG. Structural and Dynamic “Portraits” of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They? Biochemistry 2017; 56:4468-4477. [DOI: 10.1021/acs.biochem.7b00453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Peter V. Dubovskii
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Maxim A. Dubinnyi
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Anastasia G. Konshina
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | | | | | - Tatyana M. Ilyasova
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Mikhail A. Shulepko
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Rita V. Chertkova
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
- Biological
Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
- Biological
Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russia
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov
Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
- Higher School of Economics, 20 Myasnitskaya, Moscow 101000, Russia
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russia
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36
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Kosciolek T, Buchan DWA, Jones DT. Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. Sci Rep 2017; 7:6999. [PMID: 28765603 PMCID: PMC5539115 DOI: 10.1038/s41598-017-07156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022] Open
Abstract
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem. Using 200 protein structural ensembles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which can predict related data (NMR order parameter, or crystallographic B-factor). FRAGFOLD-IDP produces very good predictions for 33.5% of cases and helps to get a better insight into the dynamics of the disordered ensembles. The results also show it is not necessary to predict the correct fold of the protein to reliably predict per-residue fluctuations. It implies that disorder is a local property and it does not depend on the fold. Our results are orthogonal to DynaMine, the only other method significantly better than the naïve prediction. We therefore combine these two using a neural network. FRAGFOLD-IDP enables better insight into backbone dynamics in IDPs and opens exciting possibilities for the design of disordered ensembles, disorder-to-order transitions, or design for protein dynamics.
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Affiliation(s)
- Tomasz Kosciolek
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel W A Buchan
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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37
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Unraveling the meaning of chemical shifts in protein NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1564-1576. [PMID: 28716441 DOI: 10.1016/j.bbapap.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022]
Abstract
Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Smith LJ, Athill R, van Gunsteren WF, Hansen N. Interpretation of Seemingly Contradictory Data: Low NMR S 2 Order Parameters Observed in Helices and High NMR S 2 Order Parameters in Disordered Loops of the Protein hGH at Low pH. Chemistry 2017; 23:9585-9591. [PMID: 28503764 DOI: 10.1002/chem.201700896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/16/2022]
Abstract
At low pH, human growth hormone (hGH) adopts a partially folded state, in which the native helices are maintained, but the long loop regions and side-chain packing become disordered. Some of the S2 order parameters for backbone N-H vectors derived from NMR relaxation measurements on hGH at low pH initially seem contradictory. Three isolated residues (15, 20, and 171) in helices A and D exhibit low order parameter values (<0.5) indicating flexibility, whereas residue 143 in the centre of a long flexible loop region has a high order parameter (0.82). Using S2 order parameter restraining MD simulations, this paradox has been resolved. Low S2 values in helices are due to the presence of a mixture of 310 -helical and α-helical hydrogen bonds. High S2 values in relatively disordered parts of a protein may be due to fluctuating networks of hydrogen bonds between the backbone and the side chains, which restrict the motion of N-H bond vectors.
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Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Roya Athill
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | | | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany
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Kukic P, Pustovalova Y, Camilloni C, Gianni S, Korzhnev DM, Vendruscolo M. Structural Characterization of the Early Events in the Nucleation–Condensation Mechanism in a Protein Folding Process. J Am Chem Soc 2017; 139:6899-6910. [DOI: 10.1021/jacs.7b01540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Carlo Camilloni
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Technische Universität Mun̈chen Institute for Advanced Study & Department of Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia
Molecolari del CNR, Dipartimento di Scienze Biochimiche “A.
Rossi Fanelli”, Sapienza Università di Roma, Rome 00185, Italy
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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40
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Pancsa R, Raimondi D, Cilia E, Vranken WF. Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity. Biophys J 2017; 110:572-583. [PMID: 26840723 DOI: 10.1016/j.bpj.2015.12.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 01/20/2023] Open
Abstract
Protein folding is in its early stages largely determined by the protein sequence and complex local interactions between amino acids, resulting in lower energy conformations that provide the context for further folding into the native state. We compiled a comprehensive data set of early folding residues based on pulsed labeling hydrogen deuterium exchange experiments. These early folding residues have corresponding higher backbone rigidity as predicted by DynaMine from sequence, an effect also present when accounting for the secondary structures in the folded protein. We then show that the amino acids involved in early folding events are not more conserved than others, but rather, early folding fragments and the secondary structure elements they are part of show a clear trend toward conserving a rigid backbone. We therefore propose that backbone rigidity is a fundamental physical feature conserved by proteins that can provide important insights into their folding mechanisms and stability.
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Affiliation(s)
- Rita Pancsa
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniele Raimondi
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elisa Cilia
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
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41
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach.
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Affiliation(s)
- Sarina Grutsch
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Sven Brüschweiler
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus Vienna Biocenter 5, Vienna, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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42
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Doyle CM, Rumfeldt JA, Broom HR, Sekhar A, Kay LE, Meiering EM. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts. Biochemistry 2016; 55:1346-61. [PMID: 26849066 DOI: 10.1021/acs.biochem.5b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.
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Affiliation(s)
| | | | | | | | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children , Toronto, Canada
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43
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Chan AH, Yi SW, Terwilliger AL, Maresso AW, Jung ME, Clubb RT. Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal: A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS. J Biol Chem 2015; 290:25461-74. [PMID: 26324714 DOI: 10.1074/jbc.m115.670984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/31/2022] Open
Abstract
The endospore forming bacterium Bacillus anthracis causes lethal anthrax disease in humans and animals. The ability of this pathogen to replicate within macrophages is dependent upon the display of bacterial surface proteins attached to the cell wall by the B. anthracis Sortase A ((Ba)SrtA) enzyme. Previously, we discovered that the class A (Ba)SrtA sortase contains a unique N-terminal appendage that wraps around the body of the protein to contact the active site of the enzyme. To gain insight into its function, we determined the NMR structure of (Ba)SrtA bound to a LPXTG sorting signal analog. The structure, combined with dynamics, kinetics, and whole cell protein display data suggest that the N terminus modulates substrate access to the enzyme. We propose that it may increase the efficiency of protein display by reducing the unproductive hydrolytic cleavage of enzyme-protein covalent intermediates that form during the cell wall anchoring reaction. Notably, a key active site loop (β7/β8 loop) undergoes a disordered to ordered transition upon binding the sorting signal, potentially facilitating recognition of lipid II.
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Affiliation(s)
- Albert H Chan
- From the Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, California 90095 and
| | - Sung Wook Yi
- From the Department of Chemistry and Biochemistry
| | - Austen L Terwilliger
- the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Anthony W Maresso
- the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Robert T Clubb
- From the Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, California 90095 and
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44
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Pustovalova Y, Kukic P, Vendruscolo M, Korzhnev DM. Probing the Residual Structure of the Low Populated Denatured State of ADA2h under Folding Conditions by Relaxation Dispersion Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2015; 54:4611-22. [DOI: 10.1021/acs.biochem.5b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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45
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Structure and membrane interactions of chionodracine, a piscidin-like antimicrobial peptide from the icefish Chionodraco hamatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1285-93. [DOI: 10.1016/j.bbamem.2015.02.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/23/2015] [Accepted: 02/27/2015] [Indexed: 12/24/2022]
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46
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Hung YF, Schwarten M, Schünke S, Thiagarajan-Rosenkranz P, Hoffmann S, Sklan EH, Willbold D, Koenig BW. Dengue virus NS4A cytoplasmic domain binding to liposomes is sensitive to membrane curvature. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1119-26. [DOI: 10.1016/j.bbamem.2015.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/23/2014] [Accepted: 01/21/2015] [Indexed: 11/17/2022]
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47
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Banigan JR, Gayen A, Cho MK, Traaseth NJ. A structured loop modulates coupling between the substrate-binding and dimerization domains in the multidrug resistance transporter EmrE. J Biol Chem 2014; 290:805-14. [PMID: 25406320 DOI: 10.1074/jbc.m114.601963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Secondary active transporters undergo large conformational changes to facilitate the efflux of substrates across the lipid bilayer. Among the smallest known transport proteins are members of the small multidrug resistance (SMR) family that are composed of four transmembrane (TM) domains and assemble into dimers. An unanswered question in the SMR field is how the dimerization domain (TM4) is coupled with the substrate-binding chamber (TM1-3). To provide insight for this essential aspect of ion-coupled transport, we carried out a structure-function study on the SMR protein EmrE using solid-state NMR spectroscopy in lipid bilayers and resistance assays in Escherichia coli. The chemical shifts for EmrE were consistent with β-strand secondary structure for the loop connecting TM3 and TM4. Based on these structural results, EmrE mutants were created to ascertain whether a specific loop length and composition were necessary for function. A linker encompassing six extra Gly residues relative to wild-type EmrE failed to give resistance; however, the number of residues in the loop was not the only criterion for a functional efflux pump. Replacement of the central hydrophobic residue with Gly (L83G) also conferred no ethidium resistance phenotype, which supported the conclusion that the structure and length of the loop were both essential for ion-coupled transport. Taken together with a bioinformatics analysis, a structured linker is likely conserved across the SMR family to play an active role in mediating the conformational switch between inward-open and outward-open states necessary for drug efflux. These findings underscore the important role loops can play in mediating efflux.
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Affiliation(s)
- James R Banigan
- From the Department of Chemistry, New York University, New York, New York 10003
| | - Anindita Gayen
- From the Department of Chemistry, New York University, New York, New York 10003
| | - Min-Kyu Cho
- From the Department of Chemistry, New York University, New York, New York 10003
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48
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Vranken WF. NMR structure validation in relation to dynamics and structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:27-38. [PMID: 25444697 DOI: 10.1016/j.pnmrs.2014.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 06/04/2023]
Abstract
NMR spectroscopy is a key technique for understanding the behaviour of proteins, especially highly dynamic proteins that adopt multiple conformations in solution. Overall, protein structures determined from NMR spectroscopy data constitute just over 10% of the Protein Data Bank archive. This review covers the validation of these NMR protein structures, but rather than describing currently available methodology, it focuses on concepts that are important for understanding where and how validation is most relevant. First, the inherent characteristics of the protein under study have an influence on quality and quantity of the distinct types of data that can be acquired from NMR experiments. Second, these NMR data are necessarily transformed into a model for use in a structure calculation protocol, and the protein structures that result from this reflect the types of NMR data used as well as the protein characteristics. The validation of NMR protein structures should therefore take account, wherever possible, of the inherent behavioural characteristics of the protein, the types of available NMR data, and the calculation protocol. These concepts are discussed in the context of 'knowledge based' and 'model versus data' validation, with suggestions for questions to ask and different validation categories to consider. The principal aim of this review is to stimulate discussion and to help the reader understand the relationships between the above elements in order to make informed decisions on which validation approaches are the most relevant in particular cases.
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Affiliation(s)
- Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Department of Structural Biology, VIB, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, BC Building, 6th Floor, CP 263, 1050 Brussels, Belgium.
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49
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Structural insight into host recognition by aggregative adherence fimbriae of enteroaggregative Escherichia coli. PLoS Pathog 2014; 10:e1004404. [PMID: 25232738 PMCID: PMC4169507 DOI: 10.1371/journal.ppat.1004404] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 08/15/2014] [Indexed: 11/19/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is a leading cause of acute and persistent diarrhea worldwide. A recently emerged Shiga-toxin-producing strain of EAEC resulted in significant mortality and morbidity due to progressive development of hemolytic-uremic syndrome. The attachment of EAEC to the human intestinal mucosa is mediated by aggregative adherence fimbria (AAF). Using X-ray crystallography and NMR structures, we present new atomic resolution insight into the structure of AAF variant I from the strain that caused the deadly outbreak in Germany in 2011, and AAF variant II from archetype strain 042, and propose a mechanism for AAF-mediated adhesion and biofilm formation. Our work shows that major subunits of AAF assemble into linear polymers by donor strand complementation where a single minor subunit is inserted at the tip of the polymer by accepting the donor strand from the terminal major subunit. Whereas the minor subunits of AAF have a distinct conserved structure, AAF major subunits display large structural differences, affecting the overall pilus architecture. These structures suggest a mechanism for AAF-mediated adhesion and biofilm formation. Binding experiments using wild type and mutant subunits (NMR and SPR) and bacteria (ELISA) revealed that despite the structural differences AAF recognize a common receptor, fibronectin, by employing clusters of basic residues at the junction between subunits in the pilus. We show that AAF-fibronectin attachment is based primarily on electrostatic interactions, a mechanism not reported previously for bacterial adhesion to biotic surfaces. Enteroaggregative Escherichia coli (EAEC) is a major cause of diarrhea worldwide and is commonly present as an infection in symptomatic travelers returning from developing countries. The attachment of EAEC to the human intestine is mediated protein filaments extending from the bacterial surface known as aggregative adherence fimbria (AAF). Here we use X-ray crystallography and nuclear magnetic resonance (NMR) structures to provide an atomic structure of the protein fibers made by the two major variants, AAF/I and AAF/II. The structures of the major subunit proteins show that the AAFs assemble into flexible, linear polymers that are capped by a single minor protein subunit at the tip. Biochemical assays reveal that the AAFs recognize a common receptor, the extracellular matrix protein fibronectin, via clusters of positively-charged amino acid residues running along the length of the fimbriae. Our structures suggest a unique mechanism based on ionic interactions for AAF-mediated receptor binding and biofilm formation.
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50
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Rizzo AA, Salerno PE, Bezsonova I, Korzhnev DM. NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response. Biochemistry 2014; 53:5895-906. [PMID: 25162118 DOI: 10.1021/bi500823h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ubiquitin-mediated interactions are critical for the cellular DNA damage response (DDR). Therefore, many DDR-related proteins contain ubiquitin-binding domains, including ubiquitin-binding zinc fingers (UBZs). The majority of these UBZ domains belong to the C2H2 (type 3 Polη-like) or C2HC (type 4 Rad18-like) family. We have used nuclear magnetic resonance (NMR) spectroscopy to characterize the binding to ubiquitin and determine the structure of the type 4 UBZ domain (UBZ4) from human Rad18, which is a key ubiquitin ligase in the DNA damage tolerance pathway responsible for monoubiquitination of the DNA sliding clamp PCNA. The Rad18-UBZ domain binds ubiquitin with micromolar affinity and adopts a β1-β2-α fold similar to the previously characterized type 3 UBZ domain (UBZ3) from the translesion synthesis DNA polymerase Polη. However, despite nearly identical structures, a disparity in the location of binding-induced NMR chemical shift perturbations shows that the Rad18-UBZ4 and Polη-UBZ3 domains bind ubiquitin in distinctly different modes. The Rad18-UBZ4 domain interacts with ubiquitin with the α-helix and strand β1 as shown by the structure of the Rad18-UBZ domain-ubiquitin complex determined in this work, while the Polη-UBZ3 domain exclusively utilizes the α-helix. Our findings suggest the existence of two classes of UBZ domains in DDR-related proteins with similar structures but unique ubiquitin binding properties and provide context for further study to establish the differential roles of these domains in the complex cellular response to DNA damage.
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Affiliation(s)
- Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
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