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Dai W, Zhan M, Gao Y, Sun H, Zou Y, Laurent R, Mignani S, Majoral JP, Shen M, Shi X. Brain delivery of fibronectin through bioactive phosphorous dendrimers for Parkinson's disease treatment via cooperative modulation of microglia. Bioact Mater 2024; 38:45-54. [PMID: 38699237 PMCID: PMC11061646 DOI: 10.1016/j.bioactmat.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Effective treatment of Parkinson's disease (PD), a prevalent central neurodegenerative disorder particularly affecting the elderly population, still remains a huge challenge. We present here a novel nanomedicine formulation based on bioactive hydroxyl-terminated phosphorous dendrimers (termed as AK123) complexed with fibronectin (FN) with anti-inflammatory and antioxidative activities. The created optimized AK123/FN nanocomplexes (NCs) with a size of 223 nm display good colloidal stability in aqueous solution and can be specifically taken up by microglia through FN-mediated targeting. We show that the AK123/FN NCs are able to consume excessive reactive oxygen species, promote microglia M2 polarization and inhibit the nuclear factor-kappa B signaling pathway to downregulate inflammatory factors. With the abundant dendrimer surface hydroxyl terminal groups, the developed NCs are able to cross blood-brain barrier (BBB) to exert targeted therapy of a PD mouse model through the AK123-mediated anti-inflammation for M2 polarization of microglia and FN-mediated antioxidant and anti-inflammatory effects, thus reducing the aggregation of α-synuclein and restoring the contents of dopamine and tyrosine hydroxylase to normal levels in vivo. The developed dendrimer/FN NCs combine the advantages of BBB-crossing hydroxyl-terminated bioactive per se phosphorus dendrimers and FN, which is expected to be extended for the treatment of different neurodegenerative diseases.
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Affiliation(s)
- Waicong Dai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Mengsi Zhan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Yue Gao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Huxiao Sun
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Yu Zou
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
- Université Toulouse, 118 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
| | - Régis Laurent
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
- Université Toulouse, 118 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
| | - Serge Mignani
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
- Université Toulouse, 118 Route de Narbonne, CEDEX 4, 31077, Toulouse, France
| | - Mingwu Shen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
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Gao Y, Dai W, Ouyang Z, Shen M, Shi X. Dendrimer-Mediated Intracellular Delivery of Fibronectin Guides Macrophage Polarization to Alleviate Acute Lung Injury. Biomacromolecules 2023; 24:886-895. [PMID: 36668816 DOI: 10.1021/acs.biomac.2c01318] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fibronectin (FN) is an essential glycoprotein in the extracellular matrix with favorable biological functions for potential applications in various biomedical fields including wound healing, regenerative medicine, tissue engineering, as well as diagnosis and treatment of cancer and inflammatory diseases. Herein, we aim to explore the influence of intracellular FN delivery on macrophage functions and its possible therapeutic applications. We prepared phenylboronic acid (PBA)-functionalized generation 5 (G5) poly(amidoamine) dendrimers (G5.NH2-PBA) as a nanocarrier to load FN, and reveal that the obtained dendrimers enable efficient intracellular delivery of FN at an optimized dendrimer-to-FN weight ratio of 8, which guides macrophages toward anti-inflammatory M2 phenotype polarization. Studies on action mechanisms show that the dendrimer-mediated FN intracellular delivery acts strongly on suppressing the nuclear factor-κB pathway, leading to reduced pro-inflammatory cytokine secretion and enhanced reactive oxygen species depletion in lipopolysaccharide (LPS)-activated macrophages. Further investigation in vivo using an LPS-induced mouse model of acute lung injury (ALI) shows that the dendrimer-mediated FN delivery can effectively alleviate the ALI symptoms through alleviation of lung inflammation and oxidation stress. Our work suggests a general approach to using dendrimers for mediating intracellular delivery of FN, thereby offering many opportunities to explore the biological functions of FN for different therapeutic applications toward inflammation-associated diseases.
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Affiliation(s)
- Yue Gao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Waicong Dai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Zhijun Ouyang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Mingwu Shen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.,CQM─Centro de Química da Madeira, Universidade da Madeira, Campus Universitário da Penteada, 9020-105 Funchal, Portugal
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Clay MC, Saleh T, Kamatham S, Rossi P, Kalodimos CG. Progress toward automated methyl assignments for methyl-TROSY applications. Structure 2022; 30:69-79.e2. [PMID: 34914892 PMCID: PMC8741727 DOI: 10.1016/j.str.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023]
Abstract
Methyl-TROSY spectroscopy has extended the reach of solution-state NMR to supra-molecular machineries over 100 kDa in size. Methyl groups are ideal probes for studying structure, dynamics, and protein-protein interactions in quasi-physiological conditions with atomic resolution. Successful implementation of the methodology requires accurate methyl chemical shift assignment, and the task still poses a significant challenge in the field. In this work, we outline the current state of technology for methyl labeling, data collection, data analysis, and nuclear Overhauser effect (NOE)-based automated methyl assignment approaches. We present MAGIC-Act and MAGIC-View, two Python extensions developed as part of the popular NMRFAM-Sparky package, and MAGIC-Net a standalone structure-based network analysis program. MAGIC-Act conducts statistically driven amino acid typing, Leu/Val pairing guided by 3D HMBC-HMQC, and NOESY cross-peak symmetry checking. MAGIC-Net provides model-based NOE statistics to aid in selection of a methyl labeling scheme. The programs provide a versatile, semi-automated framework for rapid methyl assignment.
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Affiliation(s)
- Mary C. Clay
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tamjeed Saleh
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Samuel Kamatham
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Paolo Rossi
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Corresponding authors: ,
| | - Charalampos G. Kalodimos
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, TN, United States,Lead Contact,Corresponding authors: ,
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Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS. Biophys J 2021; 120:3664-3675. [PMID: 34310942 DOI: 10.1016/j.bpj.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 11/23/2022] Open
Abstract
Na+/Ca2+ exchangers (NCXs) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+ sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the NCX of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant interdomain flexibility in the apo state but assume rigid interdomain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N residual dipolar couplings), and small-angle x-ray scattering (SAXS) data in a combined strategy to select an ensemble of conformations in agreement with the experimental data. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, whereas the wide-open interdomain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble toward extended conformers, which could be a key step in the NCXs' allosteric regulation mechanism. This strategy, combining MD with NMR and SAXS, provides a powerful approach to select ensembles of conformations that could be applied to other flexible multidomain systems.
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Profile of Matrix-Remodeling Proteinases in Osteoarthritis: Impact of Fibronectin. Cells 2019; 9:cells9010040. [PMID: 31877874 PMCID: PMC7017325 DOI: 10.3390/cells9010040] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
The extracellular matrix (ECM) is a complex and specialized three-dimensional macromolecular network, present in nearly all tissues, that also interacts with cell surface receptors on joint resident cells. Changes in the composition and physical properties of the ECM lead to the development of many diseases, including osteoarthritis (OA). OA is a chronic degenerative rheumatic disease characterized by a progressive loss of synovial joint function as a consequence of the degradation of articular cartilage, also associated with alterations in the synovial membrane and subchondral bone. During OA, ECM-degrading enzymes, including urokinase-type plasminogen activator (uPA), matrix metalloproteinases (MMPs), and a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTSs), cleave ECM components, such as fibronectin (Fn), generating fibronectin fragments (Fn-fs) with catabolic properties. In turn, Fn-fs promote activation of these proteinases, establishing a degradative and inflammatory feedback loop. Thus, the aim of this review is to update the contribution of ECM-degrading proteinases to the physiopathology of OA as well as their modulation by Fn-fs.
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7
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Wang K, Sun M, Cui D, Shen T, Wu A, Xu X. Accurate prediction of nuclear magnetic resonance shielding constants: An extension of the focal-point analysis method for magnetic parameter calculations (FPA-M) with improved efficiency. J Chem Phys 2018; 149:184101. [PMID: 30441917 DOI: 10.1063/1.5041979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously, we have proposed a method, FPA-M, for focal-point analysis of magnetic parameter calculations [Sun et al., J. Chem. Phys. 138, 124113 (2013)], where the shielding constants at equilibrium geometries σe are calculated with the second order Møller-Plesset perturbation (MP2) approach, which are extrapolated to the complete basis set (CBS) limit and then augmented by the [σe(CCSD(T)) - σe(MP2)] difference at a valence triple-ζ (VTZ) basis set, where CCSD(T) stands for the coupled cluster singles and doubles model with a perturbative correction for triple excitations. This FPA-M(MP2) method provides satisfactory results to approach to the corresponding CCSD(T)/CBS values for elements of the first two rows in the periodic tables. A series of extensions have been explored here, which replace the MP2/CBS with the Hartree-Fock (HF)/CBS for efficiency. In particular, the [σe(CCSD(T)) - σe(MP2)] VTZ difference is replaced by a step-wise correction from the [σe(CCSD(T)) - σe(MP2)] difference at a valence double-ζ basis set plus the [σe(MP2) - σe(HF)] VTZ difference, leading to a new scheme, denoted here as FPA-M(HF'). A systematical comparison has demonstrated that the FPA-M(HF') method provides an excellent balance between accuracy and efficiency, which makes routinely accurate calculations of the shielding constants for medium-sized organic molecules and biomolecules feasible.
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Affiliation(s)
- Kangli Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Meng Sun
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Deng Cui
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Tonghao Shen
- MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Anan Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Xin Xu
- MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
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8
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Monneau YR, Rossi P, Bhaumik A, Huang C, Jiang Y, Saleh T, Xie T, Xing Q, Kalodimos CG. Automatic methyl assignment in large proteins by the MAGIC algorithm. JOURNAL OF BIOMOLECULAR NMR 2017; 69:215-227. [PMID: 29098507 PMCID: PMC5764113 DOI: 10.1007/s10858-017-0149-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/23/2017] [Indexed: 05/03/2023]
Abstract
Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.
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Affiliation(s)
- Yoan R Monneau
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
| | - Paolo Rossi
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Anusarka Bhaumik
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Chengdong Huang
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yajun Jiang
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tamjeed Saleh
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tao Xie
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Qiong Xing
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charalampos G Kalodimos
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Zhang D, Lee J, Kilian KA. Synthetic Biomaterials to Rival Nature's Complexity-a Path Forward with Combinatorics, High-Throughput Discovery, and High-Content Analysis. Adv Healthc Mater 2017; 6. [PMID: 28841770 DOI: 10.1002/adhm.201700535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/08/2017] [Indexed: 12/18/2022]
Abstract
Cells in tissue receive a host of soluble and insoluble signals in a context-dependent fashion, where integration of these cues through a complex network of signal transduction cascades will define a particular outcome. Biomaterials scientists and engineers are tasked with designing materials that can at least partially recreate this complex signaling milieu towards new materials for biomedical applications. In this progress report, recent advances in high throughput techniques and high content imaging approaches that are facilitating the discovery of efficacious biomaterials are described. From microarrays of synthetic polymers, peptides and full-length proteins, to designer cell culture systems that present multiple biophysical and biochemical cues in tandem, it is discussed how the integration of combinatorics with high content imaging and analysis is essential to extracting biologically meaningful information from large scale cellular screens to inform the design of next generation biomaterials.
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Affiliation(s)
- Douglas Zhang
- Department of Materials Science and Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Junmin Lee
- Department of Materials Science and Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Kristopher A. Kilian
- Department of Materials Science and Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
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Chhum P, Yu H, An B, Doyon BR, Lin YS, Brodsky B. Consequences of Glycine Mutations in the Fibronectin-binding Sequence of Collagen. J Biol Chem 2016; 291:27073-27086. [PMID: 27799304 DOI: 10.1074/jbc.m116.753566] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Indexed: 11/06/2022] Open
Abstract
Collagen and fibronectin (Fn) are two key extracellular matrix proteins, which are known to interact and jointly shape matrix structure and function. Most proteins that interact with collagen bind only to the native triple-helical form, whereas Fn is unusual in binding strongly to denatured collagen and more weakly to native collagen. The consequences of replacing a Gly by Ser at each position in the required (Gly-Xaa-Yaa)6 Fn-binding sequence are probed here, using model peptides and a recombinant bacterial collagen system. Fluorescence polarization and solid-state assays indicated that Gly replacements at four sites within the Fn-binding sequence led to decreased Fn binding to denatured collagen. Molecular dynamics simulations showed these Gly replacements interfered with the interaction of a collagen β-strand with the β-sheet structure of Fn modules seen in the high resolution crystal structure. Whereas previous studies showed that Gly to Ser mutations within an integrin-binding site caused no major structural perturbations, mutations within the Fn-binding site caused the triple helix to become highly sensitive to trypsin digestion. This trypsin susceptibility is consistent with the significant local unfolding and loss of hydrogen bonding seen in molecular dynamics simulations. Protease sensitivity resulting from mutations in the Fn-binding sequence could lead to degradation of type I collagen, early embryonic lethality, and the scarcity of reported osteogenesis imperfecta mutations in this region.
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Affiliation(s)
| | - Hongtao Yu
- From the Departments of Biomedical Engineering and.,Chemistry, Tufts University, Medford, Massachusetts 02155
| | - Bo An
- From the Departments of Biomedical Engineering and
| | | | - Yu-Shan Lin
- Chemistry, Tufts University, Medford, Massachusetts 02155
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Hymes JP, Klaenhammer TR. Stuck in the Middle: Fibronectin-Binding Proteins in Gram-Positive Bacteria. Front Microbiol 2016; 7:1504. [PMID: 27713740 PMCID: PMC5031765 DOI: 10.3389/fmicb.2016.01504] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/08/2016] [Indexed: 11/13/2022] Open
Abstract
Fibronectin is a multidomain glycoprotein found ubiquitously in human body fluids and extracellular matrices of a variety of cell types from all human tissues and organs, including intestinal epithelial cells. Fibronectin plays a major role in the regulation of cell migration, tissue repair, and cell adhesion. Importantly, fibronectin also serves as a common target for bacterial adhesins in the gastrointestinal tract. Fibronectin-binding proteins (FnBPs) have been identified and characterized in a wide variety of host-associated bacteria. Single bacterial species can contain multiple, diverse FnBPs. In pathogens, some FnBPs contribute to virulence via host cell attachment, invasion, and interference with signaling pathways. Although FnBPs in commensal and probiotic strains are not sufficient to confer virulence, they are essential for attachment to their ecological niches. Here we describe the interaction between human fibronectin and bacterial adhesins by highlighting the FnBPs of Gram-positive pathogens and commensals. We provide an overview of the occurrence and diversity of FnBPs with a focus on the model pathogenic organisms in which FnBPs are most characterized. Continued investigation of FnBPs is needed to fully understand their divergence and specificity in both pathogens and commensals.
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Affiliation(s)
- Jeffrey P Hymes
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University Raleigh, NC, USA
| | - Todd R Klaenhammer
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University Raleigh, NC, USA
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12
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Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016; 17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023] Open
Abstract
Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.
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13
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Monneau YR, Ishida Y, Rossi P, Saio T, Tzeng SR, Inouye M, Kalodimos CG. Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications. JOURNAL OF BIOMOLECULAR NMR 2016; 65:99-108. [PMID: 27255761 PMCID: PMC4936824 DOI: 10.1007/s10858-016-0041-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 05/03/2023]
Abstract
A simple and cost effective method to independently and stereo-specifically incorporate [(1)H,(13)C]-methyls in Leu and Val in proteins is presented. Recombinant proteins for NMR studies are produced using a tailored set of auxotrophic E. coli strains. NMR active isotopes are routed to either Leu or Val methyl groups from the commercially available and scrambling-free precursors α-ketoisovalerate and acetolactate. The engineered strains produce deuterated proteins with stereospecific [(1)H,(13)C]-methyl labeling separately at Leu or Val amino acids. This is the first method that achieves Leu-specific stereospecific [(1)H,(13)C]-methyl labeling of proteins and scramble-free Val-specific labeling. Use of auxotrophs drastically decreases the amount of labeled precursor required for expression without impacting the yield. The concept is extended to Thr methyl labeling by means of a Thr-specific auxotroph that provides enhanced efficiency for use with the costly L-[4-(13)C,2,3-(2)H2,(15)N]-Thr reagent. The Thr-specific strain allows for the production of Thr-[(13)CH3](γ2) labeled protein with an optimal isotope incorporation using up to 50 % less labeled Thr than the traditional E. coli strain without the need for (2)H-glycine to prevent scrambling.
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Affiliation(s)
- Yoan R Monneau
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yojiro Ishida
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Paolo Rossi
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
- Deparment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Shiou-Ru Tzeng
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Masayori Inouye
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Charalampos G Kalodimos
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA.
- Deparment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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Abstract
Fibronectin is a large vertebrate glycoprotein that is found in soluble and insoluble forms and involved in diverse processes. Protomeric fibronectin is a dimer of subunits, each of which comprises 29-31 modules - 12 type I, two type II and 15-17 type III. Plasma fibronectin is secreted by hepatocytes and circulates in a compact conformation before it binds to cell surfaces, converts to an extended conformation and is assembled into fibronectin fibrils. Here we review biophysical and structural studies that have shed light on how plasma fibronectin transitions from the compact to the extended conformation. The three types of modules each have a well-organized secondary and tertiary structure as defined by NMR and crystallography and have been likened to "beads on a string". There are flexible sequences in the N-terminal tail, between the fifth and sixth type I modules, between the first two and last two of the type III modules, and at the C-terminus. Several specific module-module interactions have been identified that likely maintain the compact quaternary structure of circulating fibronectin. The quaternary structure is perturbed in response to binding events, including binding of fibronectin to the surface of vertebrate cells for fibril assembly and to bacterial adhesins.
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Affiliation(s)
- Lisa M Maurer
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
| | - Wenjiang Ma
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
| | - Deane F Mosher
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
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15
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Zhang D, Sun MB, Lee J, Abdeen AA, Kilian KA. C
ell shape and the presentation of adhesion ligands guide smooth muscle myogenesis. J Biomed Mater Res A 2016; 104:1212-20. [DOI: 10.1002/jbm.a.35661] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/07/2016] [Accepted: 01/19/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Douglas Zhang
- Department of Materials Science and EngineeringUniversity of Illinois at Urbana‐ChampaignUrbana Illinois
| | - Michael B. Sun
- Department of Materials Science and EngineeringUniversity of Illinois at Urbana‐ChampaignUrbana Illinois
| | - Junmin Lee
- Department of Materials Science and EngineeringUniversity of Illinois at Urbana‐ChampaignUrbana Illinois
| | - Amr A. Abdeen
- Department of Materials Science and EngineeringUniversity of Illinois at Urbana‐ChampaignUrbana Illinois
| | - Kristopher A. Kilian
- Department of Materials Science and EngineeringUniversity of Illinois at Urbana‐ChampaignUrbana Illinois
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16
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Jia FY, Ran M, Zhang B. Theoretical study on the influence of different para-substituents on 13C NMR of the single carbonyl curcumin analogues. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024415130208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Andrałojć W, Berlin K, Fushman D, Luchinat C, Parigi G, Ravera E, Sgheri L. Information content of long-range NMR data for the characterization of conformational heterogeneity. JOURNAL OF BIOMOLECULAR NMR 2015; 62:353-71. [PMID: 26044033 PMCID: PMC4782772 DOI: 10.1007/s10858-015-9951-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/25/2015] [Indexed: 05/16/2023]
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Konstantin Berlin
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze,
CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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18
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Tiouajni M, Durand D, Blondeau K, Graille M, Urvoas A, Valerio-Lepiniec M, Guellouz A, Aumont-Nicaise M, Minard P, van Tilbeurgh H. Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi. FEBS J 2014; 281:5513-31. [PMID: 25290767 DOI: 10.1111/febs.13092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/24/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
Streptococcus equi is a horse pathogen belonging to Lancefield group C. Infection by S. equi ssp. equi causes strangles, a serious and highly contagious disease of the upper respiratory tract. S. equi ssp. equi secretes a fibronectin (Fn)-binding protein, FNE, that does not contain cell wall-anchoring motifs. FNE binds to the gelatin-binding domain (GBD) of Fn, composed of the motifs (6) FI (12) FII (789) FI . FNE lacks the canonical Fn-binding peptide repeats observed in many microbial surface components recognizing adhesive matrix molecules. We found that the interaction between FNE and the human GBD is mediated by the binding of the disordered C-terminal region (residues 208-262) of FNE to the (789) FI GBD subfragment. The crystal structure of FNE showed that it is similar to the minor pilus protein Spy0125 of Streptococcus pyogenes, found at the end of pilus polymers and responsible for adhesion. FNE and Spy0125 both have a superimposable internal thioester bond between highly conserved Cys and Gln residues. Small-angle X-ray scattering of the FNE-(789) FI complex provided a model that aligns the C-terminal peptide of FNE with the E-strands of the FI domains, adopting the β-zipper extension model observed in previous structures of microbial surface components recognizing adhesive matrix molecule adhesion peptides bound to FI domains.
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Affiliation(s)
- Mounira Tiouajni
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Université Paris Sud, Orsay, France
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19
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Andrałojć W, Luchinat C, Parigi G, Ravera E. Exploring regions of conformational space occupied by two-domain proteins. J Phys Chem B 2014; 118:10576-87. [PMID: 25144917 DOI: 10.1021/jp504820w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The presence of heterogeneity in the interdomain arrangement of several biomolecules is required for their function. Here we present a method to obtain crucial clues to distinguish between different kinds of protein conformational distributions based on experimental NMR data. The method explores subregions of the conformational space and provides both upper and lower bounds of probability for the system to be in each subregion.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance, University of Florence , Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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20
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Stoffels JMJ, Hoekstra D, Franklin RJM, Baron W, Zhao C. The EIIIA domain from astrocyte-derived fibronectin mediates proliferation of oligodendrocyte progenitor cells following CNS demyelination. Glia 2014; 63:242-56. [PMID: 25156142 PMCID: PMC4737254 DOI: 10.1002/glia.22748] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022]
Abstract
Central nervous system remyelination by oligodendrocyte progenitor cells (OPCs) ultimately fails in the majority of multiple sclerosis (MS) lesions. Remyelination benefits from transient expression of factors that promote migration and proliferation of OPCs, which may include fibronectin (Fn). Fn is present in demyelinated lesions in two major forms; plasma Fn (pFn), deposited following blood‐brain barrier disruption, and cellular Fn, synthesized by resident glial cells and containing alternatively spliced domains EIIIA and EIIIB. Here, we investigated the distinctive roles that astrocyte‐derived Fn (aFn) and pFn play in remyelination. We used an inducible Cre‐lox recombination strategy to selectively remove pFn, aFn or both from mice, and examined the impact on remyelination of toxin‐induced demyelinated lesions of spinal cord white matter. This approach revealed that astrocytes are a major source of Fn in demyelinated lesions. Furthermore, following aFn conditional knockout, the number of OPCs recruited to the demyelinated lesion decreased significantly, whereas OPC numbers were unaltered following pFn conditional knockout. However, remyelination completed normally following conditional knockout of aFn and pFn. Both the EIIIA and EIIIB domains of aFn were expressed following demyelination, and in vitro assays demonstrated that the EIIIA domain of aFn mediates proliferation of OPCs, but not migration. Therefore, although the EIIIA domain from aFn mediates OPC proliferation, aFn is not essential for successful remyelination. Since previous findings indicated that astrocyte‐derived Fn aggregates in chronic MS lesions inhibit remyelination, aFn removal may benefit therapeutic strategies to promote remyelination in MS. GLIA 2015;63:242–256 We investigated the roles of cellular and plasma fibronectin in remyelination, and found that astrocyte‐derived fibronectin mediates oligodendrocyte progenitor cell proliferation in a toxin‐induced demyelination model, likely via the EIIIA domain.
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Affiliation(s)
- Josephine M J Stoffels
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, The Netherlands
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21
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Santos MF, Braga CB, Rozada TC, Basso EA, Fiorin BC. Rotational isomerism of some chloroacetamides: theoretical and experimental studies through calculations, infrared and NMR. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 129:148-156. [PMID: 24727174 DOI: 10.1016/j.saa.2014.02.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/04/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
The geometries involved in the conformational equilibria of 2,2-dichloro-N-cyclohexyl-N-methyl-acetamide (DCCMA) and 2-chloro-N,N-dicyclohexylacetamide (CDCA) were investigated. Theoretical calculations at the B3LYP/cc-pVDZ level of theory showed that gauche forms (ClCCO) are the most stable and the predominant conformers in isolated phase. Both compounds had the conformational behavior in solvents of different polarities estimated from theoretical calculations with the PCM (Polarizable Continuum Model), at the same level of theory, using infrared data from deconvolution of the carbonyl absorption bands and (13)C NMR spectra. Their IR spectra showed two carbonyl absorptions and that the conformer with the highest dipole moment had its population increased when the most polar solvents were used, in accordance with the theoretical calculation in solution. (1)JCH coupling constants were obtained from their NMR spectra, and revealed that there was population variation of conformers with solvent exchange. Experimental data (NMR and IR) as well as calculations including the solvent effects followed the same trend.
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Affiliation(s)
- Marcela F Santos
- Departamento de Química, Universidade Estadual de Ponta Grossa/UEPG, Av. General Carlos Cavalcanti 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Carolyne B Braga
- Departamento de Química, Universidade Estadual de Ponta Grossa/UEPG, Av. General Carlos Cavalcanti 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Thiago C Rozada
- Departamento de Química, Universidade Estadual de Maringá/UEM, Av. Colombo 5790, 87020-900 Maringá, PR, Brazil
| | - Ernani A Basso
- Departamento de Química, Universidade Estadual de Maringá/UEM, Av. Colombo 5790, 87020-900 Maringá, PR, Brazil
| | - Barbara C Fiorin
- Departamento de Química, Universidade Estadual de Ponta Grossa/UEPG, Av. General Carlos Cavalcanti 4748, 84030-900 Ponta Grossa, PR, Brazil.
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22
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WEN BIN, SHI YUNYU, ZHANG ZHIYONG. CLUSTERING MULTI-DOMAIN PROTEIN STRUCTURES IN THE ESSENTIAL DYNAMICS SUBSPACE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A multi-domain protein is able to exist as equilibrium of different conformations in solution, which may be critical to its biological function. Besides experimental techniques, computational methods like molecular dynamics (MD) simulations are suitable to study inter-domain motions of the protein and sample different conformational states. A MD simulation usually generates a trajectory containing large amount of protein structures, and a post-processing cluster analysis would be necessary to group similar structures into clusters and identify these typical conformations of the multi-domain protein. In this paper, the widely used k-means clustering algorithm is implemented in the protein essential dynamics (ED) subspace defined by principal component analysis on the MD trajectory. Cluster analysis of the formin binding protein 21 (FBP21) tandem WW domains demonstrate that the k-means clustering results by measuring distances between structures in the ED subspace are superior to those by using other metrics like pairwise inter-domain residue distances.
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Affiliation(s)
- BIN WEN
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - YUNYU SHI
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - ZHIYONG ZHANG
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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23
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Maciejewski M, Barlow PN, Tjandra N. Decoding the components of dynamics in three-domain proteins. J Comput Chem 2013; 35:518-25. [PMID: 24323885 DOI: 10.1002/jcc.23510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/07/2013] [Accepted: 11/24/2013] [Indexed: 01/05/2023]
Abstract
In this study, we examine the feasibility and limitations of describing the motional behavior of three-domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three-domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model-free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations.
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Affiliation(s)
- Mateusz Maciejewski
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts, 02139
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24
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Russo L, Maestre-Martinez M, Wolff S, Becker S, Griesinger C. Interdomain dynamics explored by paramagnetic NMR. J Am Chem Soc 2013; 135:17111-20. [PMID: 24111622 DOI: 10.1021/ja408143f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An ensemble-based approach is presented to explore the conformational space sampled by a multidomain protein showing moderate interdomain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Ca(v)1.2 (IQ), which adopts three different interdomain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts and paramagnetically induced residual dipolar couplings for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD-derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross-validate optimally against unused paramagnetic data. Alternative approaches led to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the interdomain dynamics and represents a general method that can be used to provide a proper ensemble description of multidomain proteins.
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Affiliation(s)
- Luigi Russo
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 37077 Göttingen, Germany
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25
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Mazzei P, Oschkinat H, Piccolo A. Reduced activity of alkaline phosphatase due to host-guest interactions with humic superstructures. CHEMOSPHERE 2013; 93:1972-1979. [PMID: 23953249 DOI: 10.1016/j.chemosphere.2013.07.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 06/29/2013] [Accepted: 07/04/2013] [Indexed: 06/02/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy was applied to directly study the interactions between the alkaline phosphatase enzyme (AP) and two different humic acids from a volcanic soil (HA-V) and a Lignite deposit (HA-L). Addition of humic matter to enzyme solutions caused signals broadening in (1)H-NMR spectra, and progressive decrease and increase of enzyme relaxation (T1 and T2) and correlation (τC) times, respectively. Spectroscopic changes were explained with formation of ever larger weakly-bound humic-enzyme complexes, whose translational and rotational motion was increasingly restricted. NMR diffusion experiments also showed that the AP diffusive properties were progressively reduced with formation of large humic-enzyme complexes. The more hydrophobic HA-L affected spectral changes more than the more hydrophilic HA-V. (1)H-NMR spectra also showed the effect of progressively greater humic-enzyme complexes on the hydrolysis of an enzyme substrate, the 4-nitrophenyl phosphate disodium salt hexahydrate (p-NPP). While AP catalysis concomitantly decreased NMR signals of p-NPP and increased those of nitrophenol, addition of humic matter progressively and significantly slowed down the rate of change for these signals. In agreement with the observed spectral changes, the AP catalytic activity was more largely inhibited by HA-L than by HA-V. Contrary to previous studies, in which humic-enzyme interactions were only indirectly assumed from changes in spectrophotometric behavior of enzyme substrates, the direct measurements of AP behavior by NMR spectroscopy indicated that humic materials formed weakly-bound host-guest complexes with alkaline phosphatase, and the enzyme catalytic activity was thereby significantly inhibited. These results suggest that the role of extracellular enzymes in soils may be considerably reduced when they come in contact with organic matter dissolved in the soil solution.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Italy
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26
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Wathen B, Jia Z. A hierarchical order within protein structures underlies large separations between strands in β-sheets. Proteins 2012; 81:163-75. [PMID: 22933362 DOI: 10.1002/prot.24173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 08/11/2012] [Accepted: 08/25/2012] [Indexed: 11/12/2022]
Abstract
Protein β-sheets often involve nonlocal interactions between parts of the polypeptide chain that are separated by hundreds of residues, raising the question of how these nonlocal contacts form. A recent study of the smallest β-sheets found that their formation was not driven by signals hidden in the primary sequence. Instead, the strands in these sheets were either local in sequence, or, when separated by large sequential distances, the intervening residues were found to fold into compact modules that anchored distant parts of the chain in close spatial proximity. Here, we examine larger β-sheets to investigate the extensibility of this principle. From an analysis of the β-sheets in a nonredundant protein dataset, we find that a highly ordered hierarchical relationship exists in the intervening structure between nonlocal β-strands. This observation is almost universal: virtually all β-sheets, no matter their complexity, appear to adopt an antiparallel model to manage the nonlocal aspects of their assembly, one where the chain, having left the vicinity of an unfinished β-sheet, retraces its steps via the same route to complete the initial sheet. Exceptions typically involve unstructured regions at chain termini. Moreover, an analysis of the residues involved in nonlocal crossstrand interactions did not produce any evidence of a signal hidden in the sequence that might direct long-range interactions. These results build on those reported for the smallest sheets, suggesting that sheet formation is either local in sequence or local in space following prior folding events that anchor disparate parts of the chain in close proximity.
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Affiliation(s)
- Brent Wathen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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27
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Tossavainen H, Koskela O, Jiang P, Ylänne J, Campbell ID, Kilpeläinen I, Permi P. Model of a Six Immunoglobulin-Like Domain Fragment of Filamin A (16–21) Built Using Residual Dipolar Couplings. J Am Chem Soc 2012; 134:6660-72. [DOI: 10.1021/ja2114882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helena Tossavainen
- Program in
Structural Biology
and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari
1, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Outi Koskela
- Laboratory of Organic Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Pengju Jiang
- Biochemistry Department, University of Oxford, Oxford, OX1 3QU
United Kingdom
- School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164 China
| | - Jari Ylänne
- Department of Biological
and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35,
FI-40014 Jyväskylä, Finland
| | - Iain D. Campbell
- Biochemistry Department, University of Oxford, Oxford, OX1 3QU
United Kingdom
| | - Ilkka Kilpeläinen
- Laboratory of Organic Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Perttu Permi
- Program in
Structural Biology
and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari
1, P.O. Box 65, FI-00014 Helsinki, Finland
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28
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To WS, Midwood KS. Plasma and cellular fibronectin: distinct and independent functions during tissue repair. FIBROGENESIS & TISSUE REPAIR 2011; 4:21. [PMID: 21923916 PMCID: PMC3182887 DOI: 10.1186/1755-1536-4-21] [Citation(s) in RCA: 379] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 09/16/2011] [Indexed: 01/01/2023]
Abstract
Fibronectin (FN) is a ubiquitous extracellular matrix (ECM) glycoprotein that plays vital roles during tissue repair. The plasma form of FN circulates in the blood, and upon tissue injury, is incorporated into fibrin clots to exert effects on platelet function and to mediate hemostasis. Cellular FN is then synthesized and assembled by cells as they migrate into the clot to reconstitute damaged tissue. The assembly of FN into a complex three-dimensional matrix during physiological repair plays a key role not only as a structural scaffold, but also as a regulator of cell function during this stage of tissue repair. FN fibrillogenesis is a complex, stepwise process that is strictly regulated by a multitude of factors. During fibrosis, there is excessive deposition of ECM, of which FN is one of the major components. Aberrant FN-matrix assembly is a major contributing factor to the switch from normal tissue repair to misregulated fibrosis. Understanding the mechanisms involved in FN assembly and how these interplay with cellular, fibrotic and immune responses may reveal targets for the future development of therapies to regulate aberrant tissue-repair processes.
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Affiliation(s)
- Wing S To
- Department of Matrix Biology, Kennedy Institute of Rheumatology Division, Nuffield Department of Orthopedic Rheumatology and Musculoskeletal Sciences, Oxford University, 65 Aspenlea Road, London, W6 8LH, UK.
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29
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Hoffmann BR, Annis DS, Mosher DF. Reactivity of the N-terminal region of fibronectin protein to transglutaminase 2 and factor XIIIA. J Biol Chem 2011; 286:32220-30. [PMID: 21757696 DOI: 10.1074/jbc.m111.255562] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transglutaminase 2 (TG2) is secreted by a non-classical pathway into the extracellular space, where it has several activities pertinent to fibronectin (FN), including binding to the gelatin-binding domain of FN and acting as an integrin co-receptor. Glutamines in the N-terminal tail of FN are known to be susceptible to transamidation by both TG2 and activated blood coagulation factor XIII (FXIIIa). We used immunoblotting, limited proteolysis, and mass spectrometry to localize glutamines within FN that are subject to TG2-catalyzed incorporation of dansylcadaverine in comparison to residues modified by FXIIIa. Such analysis of plasma FN indicated that Gln-3, Gln-7, and Gln-9 in the N-terminal tail and Gln-246 of the linker between fifth and sixth type I modules ((5)F1 and (6)F1) are transamidated by both enzymes. Only minor incorporation of dansylcadaverine was detected elsewhere. Labeling of C-terminally truncated FN constructs revealed efficient TG2- or FXIIIa-catalyzed dansylcadaverine incorporation into the N-terminal residues of constructs as small as the 29-kDa fragment that includes (1-5)F1 and lacks modules from the adjacent gelatin-binding domain. However, when only (1-3)F1 were present, dansylcadaverine incorporation into the N-terminal residues of FN was lost and instead was in the enzymes, near the active site of TG2 and terminal domains of FXIIIa. Thus, these results demonstrate that FXIIIa and TG2 act similarly on glutamines at either end of (1-5)F1 and transamidation specificity of both enzymes is achieved through interactions with the intact 29K fragment.
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Affiliation(s)
- Brian R Hoffmann
- Department of Biomolecular Chemistry and Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Walsh JD, Meier K, Ishima R, Gronenborn AM. NMR studies on domain diffusion and alignment in modular GB1 repeats. Biophys J 2011; 99:2636-46. [PMID: 20959105 DOI: 10.1016/j.bpj.2010.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/11/2010] [Accepted: 08/13/2010] [Indexed: 11/18/2022] Open
Abstract
Modular proteins contain individual domains that are often connected by flexible, unstructured linkers. Using a model system based on the GB1 domain, we constructed tandem repeat proteins and investigated the rotational diffusion and long-range angular ordering behavior of individual domains by measuring NMR relaxation parameters and residual dipolar couplings. Although they display almost identical protein-solvent interfaces, each domain exhibits distinct rotational diffusion and alignment properties. The diffusion tensor anisotropy of the N-terminal domain (NTD) is D(‖)/D(⊥) = 1.5-1.6, similar to that of single-GB1 domains (D(‖)/D(⊥) = 1.6-1.7), whereas the value for the C-terminal domain (CTD) is D(‖)/D(⊥) = 2.0-2.2. In addition, the two domains have different rotational correlation times. These effects are observed for linkers of three to 24 residues, irrespective of linker length. The NTD and CTD also differ in their degree of magnetic alignment, even with a flexible linker of 18 residues, exhibiting D(a) values of 7.7 Hz and 9.7 Hz, respectively. Our results suggest that diffusion differences and long-range influences may persist in modular protein systems, even for systems that have highly flexible linkers and exhibit no domain-domain or domain-linker interactions.
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Affiliation(s)
- Joseph D Walsh
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pennsylvania, USA
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31
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Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation. Biophys J 2010; 98:2374-82. [PMID: 20483347 DOI: 10.1016/j.bpj.2010.02.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/28/2010] [Accepted: 02/04/2010] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the (15)N relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.
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32
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Blackledge M. Mapping the conformational mobility of multidomain proteins. Biophys J 2010; 98:2043-4. [PMID: 20483310 DOI: 10.1016/j.bpj.2010.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 02/26/2010] [Accepted: 03/02/2010] [Indexed: 11/18/2022] Open
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33
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Wathen B, Jia Z. Protein beta-sheet nucleation is driven by local modular formation. J Biol Chem 2010; 285:18376-84. [PMID: 20382979 DOI: 10.1074/jbc.m110.120824] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite its central role in the protein folding process, the specific mechanism(s) behind beta-sheet formation has yet to be determined. For example, whether the nucleation of beta-sheets, often containing strands separated in sequence by many residues, is local or not remains hotly debated. Here, we investigate the initial nucleation step of beta-sheet formation by performing an analysis of the smallest beta-sheets in a non-redundant dataset on the grounds that the smallest sheets, having undergone little growth after nucleation, will be enriched for nucleating characteristics. We find that the residue propensities are similar for small and large beta-sheets as are their interstrand pairing preferences, suggesting that nucleation is not primarily driven by specific residues or interacting pairs. Instead, an examination of the structural environments of the two-stranded sheets shows that virtually all of them are contained in single, compact structural modules, or when multiple modules are present, one or both of the chain termini are involved. We, therefore, find that beta-nucleation is a local phenomenon resulting either from sequential or topological proximity. We propose that beta-nucleation is a result of two opposite factors; that is, the relative rigidity of an associated folding module that holds two stretches of coil close together in topology coupled with sufficient chain flexibility that enables the stretches of coil to bring their backbones in close proximity. Our findings lend support to the hydrophobic zipper model of protein folding (Dill, K. A., Fiebig, K. M., and Chan, H. S. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 1942-1946). Implications for protein folding are discussed.
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Affiliation(s)
- Brent Wathen
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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34
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35
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Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:769-80. [DOI: 10.1007/s00249-009-0549-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 09/10/2009] [Accepted: 09/24/2009] [Indexed: 01/08/2023]
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36
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Etzkorn M, Kneuper H, Dünnwald P, Vijayan V, Krämer J, Griesinger C, Becker S, Unden G, Baldus M. Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS. Nat Struct Mol Biol 2008; 15:1031-9. [DOI: 10.1038/nsmb.1493] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 08/29/2008] [Indexed: 11/09/2022]
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37
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Soroka V, Kasper C, Poulsen FM. WITHDRAWN: Structural Biology of NCAM. Neurochem Res 2008. [PMID: 18758952 DOI: 10.1007/s11064-008-9837-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2008] [Indexed: 01/18/2023]
Affiliation(s)
- Vladislav Soroka
- Protein Laboratory, Institute of Neuroscience and Pharmacology, Panum Institute, Blegdamsvej 3 C, DK-2200, Copenhagen, Denmark,
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38
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Korukottu J, Schneider R, Vijayan V, Lange A, Pongs O, Becker S, Baldus M, Zweckstetter M. High-resolution 3D structure determination of kaliotoxin by solid-state NMR spectroscopy. PLoS One 2008; 3:e2359. [PMID: 18523586 PMCID: PMC2387072 DOI: 10.1371/journal.pone.0002359] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 04/18/2008] [Indexed: 11/19/2022] Open
Abstract
High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from 1H/1H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 Å and 1.3 Å for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins.
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Affiliation(s)
- Jegannath Korukottu
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Robert Schneider
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vinesh Vijayan
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Olaf Pongs
- Zentrum für Molekulare Neurobiologie, Institut für Neurale Signalverarbeitung, Hamburg, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marc Baldus
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail: (MB); (MZ)
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail: (MB); (MZ)
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39
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Shi Y, Wu J. Structural basis of protein–protein interaction studied by NMR. ACTA ACUST UNITED AC 2007; 8:67-72. [PMID: 17763922 DOI: 10.1007/s10969-007-9021-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 07/17/2007] [Indexed: 01/02/2023]
Abstract
This paper describes efforts of the structural genomics project in the nuclear magnetic resonance (NMR) laboratory at the University of Science and Technology of China. This structural genomics project is biological-functional driven. Targets are mainly selected from two systems: proteins related with regulation of gene expression in humans and other eukaryotes, and proteins existing in the cell junction in humans. The majority of proteins selected from these two systems are related with human health and diseases, and some are potential drug targets. Twenty-five protein structures from Homo sapiens and other eukaryotes have been determined during last 5 years in this laboratory. Nuclear magnetic resonance (NMR) spectroscopy is highly suited to investigate molecular interactions at a close physiological condition and is particularly suited for the study of low-affinity, transient complexes. It can provide information on protein surface interaction, their complex structure, and their dynamic properties during protein recognition. Several examples are given in this paper.
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Affiliation(s)
- Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
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40
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Abstract
Domain mobility plays an essential role in the biological function of multidomain systems. The characteristic times of domain motions fall into the interval from nano- to milliseconds, amenable to NMR studies. Proper analysis of NMR relaxation data for these systems in solution has to account for interdomain motions, in addition to the overall tumbling and local intradomain dynamics. Here we propose a model of interdomain mobility in a multidomain protein, which considers domain reorientations as exchange/interconversion between two distinct conformational states of the molecule, combined with fully anisotropic overall tumbling. Analysis of 15N-relaxation data for Lys48-linked diubiquitin at pH 4.5 and 6.8 showed that this model adequately fits the experimental data and allows characterization of both structural and motional properties of diubiquitin, thus providing information about the relative orientation of ubiquitin domains in both interconverting states. The analysis revealed that the two domains reorient on a time scale of 9-30 ns, with the amplitudes sufficient for allowing a protein ligand access to the binding sites sequestered at the interface in the closed conformation. The analysis of a possible mechanism controlling the equilibrium between the interconverting states in diubiquitin points toward protonation of His68, which results in three different charged states of the molecule, with zero, +e, and +2e net charge. Only two of the three states are noticeably populated at pH 4.5 or 6.8, which assures applicability of the two-state model to diubiquitin at these conditions. We also compare our model with the "extended model-free" approach and discuss possible future developments of the model.
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Affiliation(s)
| | - David Fushman
- All correspondence should be addressed to, David Fushman, 1115 Biomolecular Sciences Bldg (#296), Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742-3360, USA, Tel: (301) 405 3461, Fax: (301) 314 0386, E-mail:
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42
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Rudiño-Piñera E, Ravelli RBG, Sheldrick GM, Nanao MH, Korostelev VV, Werner JM, Schwarz-Linek U, Potts JR, Garman EF. The solution and crystal structures of a module pair from the Staphylococcus aureus-binding site of human fibronectin--a tale with a twist. J Mol Biol 2007; 368:833-44. [PMID: 17368672 DOI: 10.1016/j.jmb.2007.02.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 02/10/2007] [Accepted: 02/16/2007] [Indexed: 10/23/2022]
Abstract
An important goal of structural studies of modular proteins is to determine the inter-module orientation, which often influences biological function. The N-terminal domain of human fibronectin (Fn) is composed of a string of five type 1 modules (F1). Despite their small size, to date F1 modules have proved intractable to X-ray structure solution, although there are several NMR structures available. Here, we present the first structures (two X-ray models and an NMR-derived model) of the (2)F1(3)F1 module pair, which forms part of the binding site for Fn-binding proteins from pathogenic bacteria. The crystallographic structure determination was aided by the novel technique of UV radiation damage-induced phasing. The individual module structures are very similar in all three models. In the NMR structure and one of the X-ray structures, a similar but smaller interdomain interface than that observed previously for (4)F1(5)F1 is seen. The other X-ray structure has a different interdomain orientation. This work underlines the benefits of combining X-ray and NMR data in the studies of multi-domain proteins.
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43
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Ryabov Y, Fushman D. Analysis of interdomain dynamics in a two-domain protein using residual dipolar couplings together with 15N relaxation data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S143-51. [PMID: 16823894 DOI: 10.1002/mrc.1822] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this paper, we propose the idea that simultaneous analysis of NMR relaxation data and residual dipolar couplings (RDCs) can provide information about interdomain dynamics in a multidomain protein, which cannot be derived from each data set separately. Specifically, such an approach can be useful when the interdomain motions occur on a timescale comparable to or slower than the overall tumbling in solution. We analyze residual dipolar couplings together with 15N relaxation data for Lys48-linked di-ubiquitin (Ub2), in which interdomain dynamics are described as interconversion between two distinct conformational states of the protein. Our results show that 15N relaxation and residual dipolar coupling data can be used as two complementary experimental data sets for consistent characterization of interdomain conformations and dynamics in this dual-domain protein.
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Affiliation(s)
- Yaroslav Ryabov
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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44
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Abstract
Domain orientation and dynamics can play an essential role in the function of multidomain proteins. Lys48-linked polyubiquitin chains, the principal signal for proteasomal protein degradation, adopt a closed conformation at physiological conditions, in which the functionally important residues Leu8, Ile44, and Val70 are sequestered at the interdomain interface. This interface must open in order for these groups to become available for interactions with various chain-recognition factors. Knowledge of the mechanism of domain motion leading to the opening of the interdomain interface in polyubiqutin is, therefore, essential for the understanding of the processes controlling molecular recognition events in polyubiquitin signaling. Here we use NMR to characterize the interdomain dynamics that open the interface in a di-ubiquitin chain. This process occurs via domain reorientations on a 10-ns time scale and with the amplitudes that are sufficient for making functionally important hydrophobic residues in polyubiquitin available for direct interactions with various ubiquitin-binding factors. The analysis revealed the structures of the interconverting conformational states of di-ubiquitin and the rates and amplitudes of this process at near-physiological and acidic pH. The proposed mechanism of domain reorientation is quite general and could serve as a paradigm of interdomain mobility in other multidomain systems.
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Affiliation(s)
- Yaroslav Ryabov
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742-3360, USA
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45
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Banerjee AL, Tobwala S, Ganguly B, Mallik S, Srivastava DK. Molecular basis for the origin of differential spectral and binding profiles of dansylamide with human carbonic anhydrase I and II. Biochemistry 2005; 44:3673-82. [PMID: 15751944 DOI: 10.1021/bi0475018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfonamide derivatives serve as potent inhibitors of carbonic anhydrases (CAs), and a few such inhibitors have been currently used as drugs for the treatment of different pathogenic conditions in humans. In pursuit of designing the isozyme-specific inhibitors of human CAs, we observed that the fluorescence spectral properties and binding profiles of a fluorogenic sulfonamide derivative, 5-(dimethylamino)-1-naphthalenesulfonamide (dansylamide, DNSA), were markedly different between the recombinant forms of human carbonic anhydrase I (hCA I) and II (hCA II). The kinetic evaluation of the overall microscopic pathways for the binding of DNSA to hCA I versus hCA II revealed that the protein isomerization step served as a major determinant of the above discrepancy. Arguments are presented that the detailed structural-functional investigations of enzyme-ligand interactions may provide insights into designing the isozyme-specific inhibitors of CAs.
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Affiliation(s)
- Abir L Banerjee
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA
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46
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Lange A, Becker S, Seidel K, Giller K, Pongs O, Baldus M. A Concept for Rapid Protein-Structure Determination by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2005; 44:2089-92. [PMID: 15744789 DOI: 10.1002/anie.200462516] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Adam Lange
- Max-Planck-Institut für Biophysikalische Chemie, Abteilung für NMR-Basierte Strukturbiologie, 37077 Göttingen, Germany
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47
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Lange A, Becker S, Seidel K, Giller K, Pongs O, Baldus M. Ein Konzept zur schnellen Bestimmung von Proteinstrukturen durch Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462516] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Etzkorn M, Böckmann A, Lange A, Baldus M. Probing Molecular Interfaces Using 2D Magic-Angle-Spinning NMR on Protein Mixtures with Different Uniform Labeling. J Am Chem Soc 2004; 126:14746-51. [PMID: 15535698 DOI: 10.1021/ja0479181] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A general NMR strategy to directly study molecular interfaces under magic angle spinning is introduced. The approach is based on the spectroscopic analysis of uniformly, but heterogeneously, labeled molecular mixtures containing the spin species X and Y (X:Y). For the case of an ((15)N:(13)C) labeled sample, the use of NC, NHC, and NHHC transfers is demonstrated. Applied to the ((13)C:(15)N) labeled dimeric form of the 85 amino acid protein Crh, the NHHC approach reveals a variety of monomer-monomer interactions in the microcrystalline state.
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Affiliation(s)
- Manuel Etzkorn
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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