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Wang Y, He S, Zhou F, Sun H, Cao X, Ye Y, Li J. Detection of Lectin Protein Allergen of Kidney Beans ( Phaseolus vulgaris L.) and Desensitization Food Processing Technology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14723-14741. [PMID: 34251800 DOI: 10.1021/acs.jafc.1c02801] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the increase of food allergy events related to not properly cooked kidney beans (Phaseolus vulgaris L.), more and more researchers are paying attention to the sensitization potential of lectin, one of the major storage and defensive proteins with the specific carbohydrate-binding activity. The immunoglobulin E (IgE), non-IgE, and mixed allergic reactions induced by the lectins were inducted in the current paper, and the detection methods of kidney bean lectin, including the purification strategies, hemagglutination activity, specific polysaccharide or glycoprotein interactions, antibody combinations, mass spectrometry methods, and allergomics strategies, were summarized, while various food processing aspects, such as the physical thermal processing, physical non-thermal processing, chemical modifications, and biological treatments, were reviewed in the potential of sensitization reduction. It might be the first comprehensive review on lectin allergen detection from kidney bean and the desensitization strategy in food processing and will provide a basis for food safety control.
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Affiliation(s)
- Yongfei Wang
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Shudong He
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Fanlin Zhou
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Hanju Sun
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Xiaodong Cao
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Yongkang Ye
- Engineering Research Center of Bio-process of Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, People's Republic of China
| | - Jing Li
- College of Biological and Environmental Engineering, Hefei University, Hefei, Anhui 230601, People's Republic of China
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2
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Gabelica V. Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand. Acc Chem Res 2021; 54:3691-3699. [PMID: 34546031 DOI: 10.1021/acs.accounts.1c00396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.
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Affiliation(s)
- Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM,
ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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3
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Köhn B, Schwarz P, Wittung-Stafshede P, Kovermann M. Impact of crowded environments on binding between protein and single-stranded DNA. Sci Rep 2021; 11:17682. [PMID: 34480058 PMCID: PMC8417293 DOI: 10.1038/s41598-021-97219-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022] Open
Abstract
The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA-protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein's hydration shell via soft interactions that, in turn, tune protein-ligand binding dynamics and affinity.
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Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Patricia Schwarz
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany. .,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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4
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Chen K, Wang Q, Fu Y, Yu X, Liu P, Kang F. Weak interaction-alleviated toxicity of aromatic compounds in EPS matrices: Quantifying the noncovalent bonding-to-EPS ecoservice chain. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125824. [PMID: 34492786 DOI: 10.1016/j.jhazmat.2021.125824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 06/13/2023]
Abstract
Extracellular polymeric substances (EPSs) constitute a largely global carbon pool that could participate in geochemical process of organic chemicals. Besides the chemical hydrolysis and redox of chemicals exerted by the EPS, weakly noncovalent interactions with dispersive EPS control the toxicity of numerous organic compounds. Nevertheless, there has been a lack of in-depth research on this issue. This work quantified a chain of links from bonding to detoxification using natural biofilms to explore the control behavior of fragile noncovalent bonding to the ecotoxicity of aromatic compounds. Such bonding decreases cell absorbability of m-phenylenediamine, 2-naphthol, and phenanthrene by 5.3-53.6%, resultantly increasing the indices of microbial diversity by 122.2-279.5%. Herein, the 60 kDa chaperonin in EPS acts as the most important contributor (16.4% of the top 20 proteins) to noncovalent interactions. Hydrophilic carboxyl groups in EPS bind with hydroxyl and amino groups of m-phenylenediamine and 2-naphthol via H-bonds, respectively. Methylene and carboxyl groups combine with hydrophobic phenanthrene via CH···π and H-bonding, respectively. A quantified chain was consequently established that weak interaction linearly controls ecotoxicity of aromatic compounds via the above suppressive cell absorbability of aromatic compounds (R2 =0.82). Considering ubiquitous EPS and prevailing aromatic compounds, our findings revealed a previously unnoticed phenomenon in which seemingly fragile noncovalent bonding profoundly alleviates the ecotoxicity of aromatic compounds in Earth's surface system.
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Affiliation(s)
- Kai Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Qian Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Jiangsu 210008, China
| | - Yaojia Fu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Xiaoxiao Yu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Peilin Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Fuxing Kang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China.
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5
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D’Souza AR, Necelis MR, Kulesha A, Caputo GA, Makhlynets OV. Beneficial Impacts of Incorporating the Non-Natural Amino Acid Azulenyl-Alanine into the Trp-Rich Antimicrobial Peptide buCATHL4B. Biomolecules 2021; 11:421. [PMID: 33809374 PMCID: PMC8001250 DOI: 10.3390/biom11030421] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial peptides (AMPs) present a promising scaffold for the development of potent antimicrobial agents. Substitution of tryptophan by non-natural amino acid Azulenyl-Alanine (AzAla) would allow studying the mechanism of action of AMPs by using unique properties of this amino acid, such as ability to be excited separately from tryptophan in a multi-Trp AMPs and environmental insensitivity. In this work, we investigate the effect of Trp→AzAla substitution in antimicrobial peptide buCATHL4B (contains three Trp side chains). We found that antimicrobial and bactericidal activity of the original peptide was preserved, while cytocompatibility with human cells and proteolytic stability was improved. We envision that AzAla will find applications as a tool for studies of the mechanism of action of AMPs. In addition, incorporation of this non-natural amino acid into AMP sequences could enhance their application properties.
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Affiliation(s)
- Areetha R. D’Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
| | - Matthew R. Necelis
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (M.R.N.); (G.A.C.)
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (M.R.N.); (G.A.C.)
- Department of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
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6
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Wang Q, Chen K, Huang S, Zhu X, Kang F. Spontaneous assembly of microbial extracellular polymeric substances into microcapsules involved in trapping and immobilizing degradation-resistant oxoanions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143651. [PMID: 33257076 DOI: 10.1016/j.scitotenv.2020.143651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/07/2020] [Accepted: 11/08/2020] [Indexed: 06/12/2023]
Abstract
Despite the ubiquity of microbial extracellular polymeric substances (EPS) in soils and aquatic environments, the roles played by EPS in the nonreductive transformation of toxic and degradation-resistant oxoanions are poorly understood. Here, we used perchlorate, which is ubiquitous in surface environments, as an initiator to study the spontaneous assembly of EPS into microcapsules involved in trapping and immobilizing oxoanions. The results confirmed that ClO4- oxoanions could be rapidly trapped in 20 min by EPS extracted from a common Bacillus subtilis, whereas no chemical reduction of ClO4- occurred in 48 h. Integrated spectroscopic analyses with florescence quenching microtitration and theoretical models showed that amino functionalities of EPS are responsible for sequestering ClO4-, with lower pH values being more favorable to formation of EPS-ClO4- micelles. Combined molecular dynamics scheme with wave function analyses showed that besides amino residues, the protonated side-chain amino groups in the basic proteins have a greater capacity for sequestering ClO4- through a noncovalent H-bonding mechanism in which dissociable protons serve as the nodes to bridge ClO4-. A quantitative association between the number of hydrogen bonds and bioavailability revealed that immobilization by EPS mitigates the uptake of toxic oxoanions by forage ryegrass, reducing their risk exposure to edible produce. MAIN FINDING OF THE WORK: Micelles formed by freely dissolved EPS mitigate the uptake of toxic oxoanions by forage ryegrass.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Jiangsu 210008, China
| | - Kai Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Shuhan Huang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Xuezhu Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Fuxing Kang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China.
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7
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Kontos C, El Bounkari O, Krammer C, Sinitski D, Hille K, Zan C, Yan G, Wang S, Gao Y, Brandhofer M, Megens RTA, Hoffmann A, Pauli J, Asare Y, Gerra S, Bourilhon P, Leng L, Eckstein HH, Kempf WE, Pelisek J, Gokce O, Maegdefessel L, Bucala R, Dichgans M, Weber C, Kapurniotu A, Bernhagen J. Designed CXCR4 mimic acts as a soluble chemokine receptor that blocks atherogenic inflammation by agonist-specific targeting. Nat Commun 2020; 11:5981. [PMID: 33239628 PMCID: PMC7689490 DOI: 10.1038/s41467-020-19764-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 10/28/2020] [Indexed: 11/22/2022] Open
Abstract
Targeting a specific chemokine/receptor axis in atherosclerosis remains challenging. Soluble receptor-based strategies are not established for chemokine receptors due to their discontinuous architecture. Macrophage migration-inhibitory factor (MIF) is an atypical chemokine that promotes atherosclerosis through CXC-motif chemokine receptor-4 (CXCR4). However, CXCR4/CXCL12 interactions also mediate atheroprotection. Here, we show that constrained 31-residue-peptides ('msR4Ms') designed to mimic the CXCR4-binding site to MIF, selectively bind MIF with nanomolar affinity and block MIF/CXCR4 without affecting CXCL12/CXCR4. We identify msR4M-L1, which blocks MIF- but not CXCL12-elicited CXCR4 vascular cell activities. Its potency compares well with established MIF inhibitors, whereas msR4M-L1 does not interfere with cardioprotective MIF/CD74 signaling. In vivo-administered msR4M-L1 enriches in atherosclerotic plaques, blocks arterial leukocyte adhesion, and inhibits atherosclerosis and inflammation in hyperlipidemic Apoe-/- mice in vivo. Finally, msR4M-L1 binds to MIF in plaques from human carotid-endarterectomy specimens. Together, we establish an engineered GPCR-ectodomain-based mimicry principle that differentiates between disease-exacerbating and -protective pathways and chemokine-selectively interferes with atherosclerosis.
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MESH Headings
- Aged
- Animals
- Antigens, CD/metabolism
- Atherosclerosis/drug therapy
- Atherosclerosis/genetics
- Atherosclerosis/pathology
- Atherosclerosis/surgery
- Binding Sites
- Carotid Artery, Common/pathology
- Carotid Artery, Common/surgery
- Chemokine CXCL12/metabolism
- Crystallography, X-Ray
- Disease Models, Animal
- Drug Design
- Drug Evaluation, Preclinical
- Endarterectomy, Carotid
- Female
- Humans
- Intramolecular Oxidoreductases/antagonists & inhibitors
- Intramolecular Oxidoreductases/metabolism
- Macrophage Migration-Inhibitory Factors/antagonists & inhibitors
- Macrophage Migration-Inhibitory Factors/metabolism
- Male
- Mice
- Mice, Knockout, ApoE
- Middle Aged
- Peptide Fragments/pharmacology
- Peptide Fragments/therapeutic use
- Receptors, CXCR4/chemistry
- Receptors, CXCR4/metabolism
- Receptors, CXCR4/ultrastructure
- Sialyltransferases/metabolism
- Signal Transduction/drug effects
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Affiliation(s)
- Christos Kontos
- Division of Peptide Biochemistry, TUM School of Life Sciences, Technische Universität München (TUM), 85354, Freising, Germany
| | - Omar El Bounkari
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Christine Krammer
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Dzmitry Sinitski
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Kathleen Hille
- Division of Peptide Biochemistry, TUM School of Life Sciences, Technische Universität München (TUM), 85354, Freising, Germany
| | - Chunfang Zan
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Guangyao Yan
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Sijia Wang
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Ying Gao
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Markus Brandhofer
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention, Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 80336, Munich, Germany
| | - Adrian Hoffmann
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
- Department of Anaesthesiology, Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Yaw Asare
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Simona Gerra
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Priscila Bourilhon
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
| | - Lin Leng
- Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Hans-Henning Eckstein
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Wolfgang E Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Jaroslav Pelisek
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
- Department of Vascular Surgery, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technische Universität München (TUM), 81675, Munich, Germany
| | - Richard Bucala
- Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention, Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 80336, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
- Munich Heart Alliance, 80802, Munich, Germany
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229, Maastricht, The Netherlands
| | - Aphrodite Kapurniotu
- Division of Peptide Biochemistry, TUM School of Life Sciences, Technische Universität München (TUM), 85354, Freising, Germany.
| | - Jürgen Bernhagen
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Ludwig-Maximilians-Universität (LMU) München, 81377, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany.
- Munich Heart Alliance, 80802, Munich, Germany.
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8
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Liyanage SH, Yan M. Quantification of binding affinity of glyconanomaterials with lectins. Chem Commun (Camb) 2020; 56:13491-13505. [PMID: 33057503 PMCID: PMC7644678 DOI: 10.1039/d0cc05899h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Carbohydrate-mediated interactions are involved in many cellular activities including immune responses and infections. These interactions are relatively weak, and as such, cells employ multivalency, i.e., the presentation of multiple monovalent carbohydrate ligands within a close proximity, for cooperative binding thus drastically enhanced binding affinity. In the past two decades, the field of glyconanomaterials has emerged where nanomaterials are used as multivalent scaffolds to present multiple copies of carbohydrate ligands on the nanomaterial surface. At the core of glyconanomaterial research is the ability to control and modulate multivalency through ligand display. For the quantitative evaluation of multivalency, the binding affinity must be determined. Quantification of the binding parameters provides insights for not only the fundamental glyconanomaterial-lectin interactions, but also the rational design of effective diagnostics and therapeutics. Several methods have been developed to determine the binding affinity of glyconanomaterials with lectins, including fluorescence competitive assays in solution or on microarrays, Förster resonance energy transfer, fluorescence quenching, isothermal titration calorimetry, surface plasmon resonance spectroscopy, quartz crystal microbalance and dynamic light scattering. This Feature Article discusses each of these techniques, as well as how each technique is applied to determine the binding affinity of glyconanomaterials with lectins, and the data analysis. Although the results differed depending on the specific method used, collectively, they showed that nanomaterials as multivalent scaffolds could amplify the binding affinity of carbohydrate-lectin interactions by several orders of magnitude, the extent of which depending on the structure of the carbohydrate ligand, the ligand density, the linker length and the particle size.
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Affiliation(s)
- Sajani H Liyanage
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, Massachusetts 01854, USA.
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9
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Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D. How to measure and evaluate binding affinities. eLife 2020; 9:e57264. [PMID: 32758356 PMCID: PMC7452723 DOI: 10.7554/elife.57264] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
Quantitative measurements of biomolecule associations are central to biological understanding and are needed to build and test predictive and mechanistic models. Given the advances in high-throughput technologies and the projected increase in the availability of binding data, we found it especially timely to evaluate the current standards for performing and reporting binding measurements. A review of 100 studies revealed that in most cases essential controls for establishing the appropriate incubation time and concentration regime were not documented, making it impossible to determine measurement reliability. Moreover, several reported affinities could be concluded to be incorrect, thereby impacting biological interpretations. Given these challenges, we provide a framework for a broad range of researchers to evaluate, teach about, perform, and clearly document high-quality equilibrium binding measurements. We apply this framework and explain underlying fundamental concepts through experimental examples with the RNA-binding protein Puf4.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Ishraq AlSadhan
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
- Stanford ChEM-H, Stanford UniversityStanfordUnited States
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10
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Yokoyama H, Mizutani R, Noguchi S, Hayashida N. Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab. Sci Rep 2019; 9:18494. [PMID: 31811216 PMCID: PMC6898713 DOI: 10.1038/s41598-019-54918-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/14/2019] [Indexed: 01/07/2023] Open
Abstract
The formation of the isoaspartate (isoAsp) is one of spontaneous degradation processes of proteins, affecting their stability and activity. Here, we report for the first time the crystal structures of an antibody Fab that contains isoAsp in the complementarity-determining region (CDR), along with biochemical studies to detect isoAsp. By comparing the elution profiles of cation-exchange chromatography, it was clarified that the antibody 64M-5 Fab is converted from the normal form to isoAsp form spontaneously and time-dependently under physiological conditions. The isoAsp residue was identified with tryptic peptide mapping, N-terminal sequencing, and the protein isoaspartyl methyltransferase assay. Based on the fluorescence quenching method, the isoAsp form of 64M-5 Fab shows a one order of magnitude lower binding constant for its dinucleotide ligand dT(6-4)T than the normal form. According to the structure of the isoAsp form, the conformation of CDR L1 is changed from the normal form to isoAsp form; the loss of hydrogen bonds involving the Asn28L side-chain, and structural conversion of the β-turn from type I to type II'. The formation of isoAsp leads to a large displacement of the side chain of His27dL, and decreased electrostatic interactions with the phosphate group of dT(6-4)T. Such structural changes should be responsible for the lower affinity of the isoAsp form for dT(6-4)T than the normal form. These findings may provide insight into neurodegenerative diseases (NDDs) and related diseases caused by misfolded proteins.
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Affiliation(s)
- Hideshi Yokoyama
- 0000 0001 0660 6861grid.143643.7Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba 278-8510 Japan
| | - Ryuta Mizutani
- 0000 0001 1516 6626grid.265061.6Graduate School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292 Japan
| | - Shuji Noguchi
- 0000 0000 9290 9879grid.265050.4Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| | - Naoki Hayashida
- 0000 0001 0660 7960grid.268397.1Division of Molecular Gerontology and Anti-Ageing Medicine, Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505 Japan
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11
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Shou W, Kang F, Huang S, Yan C, Zhou J, Wang Y. Substituted Aromatic-Facilitated Dissemination of Mobile Antibiotic Resistance Genes via an Antihydrolysis Mechanism Across an Extracellular Polymeric Substance Permeable Barrier. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:604-613. [PMID: 30562461 DOI: 10.1021/acs.est.8b05750] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mobile antibiotic resistance genes (ARGs) in environmental systems may pose a threat to public health. The coexisting substituted aromatic pollutants may help the ARGs cross the extracellular polymeric substance (EPS) permeable barrier into the interior of cells, facilitating ARG dissemination, but the mechanism is still unknown. Here, we demonstrated that a specific antihydrolysis mechanism of mobile plasmid in the extracellular matrix makes a greater contribution to this facilitated dissemination. Specifically, fluorescence microtitration with a Tb3+-labeled pUC19 plasmid was used to study the formation of substituted aromatic-plasmid complexes associated with ARG dissemination. Manipulations of the endA gene and an EPS confirmed that these forming complexes antagonize the EPS-mediated hydrolysis of the plasmid. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and computational chemistry demonstrated that substituents alter the polarity of aromatic molecules, making the carbon at the 6-position of 1,3-dichlorobenzene as well as the labile protons (-NH2/-OH) of m-phenylenediamine, aniline, and 2-naphthol interact with the deprotonated hydroxy group of the phosphate (P-O···H-C/N/O), mainly via hydrogen bonds. Linear correlations among ARG disseminations, association constants, and bonding energies highlight the quantitative dependency of ARG proliferation on a combination of functionalities templated by d-ribose-phosphate.
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Affiliation(s)
- Weijun Shou
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
| | - Fuxing Kang
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
| | - Shuhan Huang
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
| | - Chunyao Yan
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
| | - Jiaxin Zhou
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
| | - Yijin Wang
- College of Resources and Environmental Sciences , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , China
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12
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Moldenhauer D, Fuenzalida Werner JP, Strassert CA, Gröhn F. Light-Responsive Size of Self-Assembled Spiropyran-Lysozyme Nanoparticles with Enzymatic Function. Biomacromolecules 2019; 20:979-991. [PMID: 30570257 DOI: 10.1021/acs.biomac.8b01605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel light-responsive nanoassemblies with switchable size and enzymatic activity are built from a protein and a water-soluble spiropyran. Assemblies are created by electrostatic self-assembly in aqueous solution such that the photochromic property of the spiropyran enables light responsiveness. Upon visible light exposure, the aggregate size increases from 200 to 400 nm. The enzyme retains its activity upon aggregation into the assembly, while it decreases through visible light irradiation. Fundamentally, we show how the two different spiropyran isomers, the open-ring merocyanine form and the closed-ring spiropyran form, bind differently to the protein, which triggers the assembly size and use of thermodynamic data to understand the binding process and the size response. Thus, as a proof of concept, a self-assembly driven light-tunable enzyme activity in conjunction with a triggerable assembly size is demonstrated for a model system. The concept bears future potential for various possible biological applications ranging from genetic control over vaccine applications to the detection of certain proteins.
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Affiliation(s)
- Daniel Moldenhauer
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Juan Pablo Fuenzalida Werner
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Cristian A Strassert
- Institute of Physics and Center for Nanotechnology , Westfälische Wilhelms-Universität Münster , Heisenbergstraße 11 , D-48149 Münster , Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
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13
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Bednarek S, Madan V, Sikorski PJ, Bartenschlager R, Kowalska J, Jemielity J. mRNAs biotinylated within the 5' cap and protected against decapping: new tools to capture RNA-protein complexes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0167. [PMID: 30397103 DOI: 10.1098/rstb.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein-RNA complexes. In conclusion, RNAs labelled with biotin via the 5' cap structure can be applied to a variety of biological experiments based on biotin-avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays, in vivo visualization, cellular delivery and many others.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Sylwia Bednarek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Vanesa Madan
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Ralf Bartenschlager
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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14
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De Filippis V, Acquasaliente L, Pontarollo G, Peterle D. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction. Biotechnol Appl Biochem 2018; 65:69-80. [DOI: 10.1002/bab.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
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15
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Dos Santos ER, Graminha AE, Schultz MS, Correia I, Selistre-de-Araújo HS, Corrêa RS, Ellena J, Lacerda EDPS, Pessoa JC, Batista AA. Cytotoxic activity and structural features of Ru(II)/phosphine/amino acid complexes. J Inorg Biochem 2017; 182:48-60. [PMID: 29433005 DOI: 10.1016/j.jinorgbio.2017.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 02/05/2023]
Abstract
Thirteen new ruthenium amino acid complexes were synthesized and characterized. They were obtained by the reaction of α-amino acids (AA) with [RuCl2(P-P)(N-N)], where P-P=1,4-bis(diphenylphosphino)butane (dppb) or 1,3-bis(diphenylphosphino)propane (dppp) and N-N=4,4'-dimethyl-2,2'-bipyridine (4'-Mebipy), 5,5'-dimethyl-2,2'-bipyridine (5'-Mebipy) or 4,4'-Methoxy-2-2'-bipyridine (4'-MeObipy). This afforded a family of complexes formulated as [Ru(AA-H)(P-P)(N-N)]PF6, where AA=glycine (Gly), L-alanine (Ala), L-valine (Val), L-tyrosine (Tyr), L-tryptophan (Trp), L-histidine (His) and L-methionine (Met). All compounds were characterized by elemental analysis, spectroscopic and electrochemical techniques. The [Ru(AA-H)(P-P)(N-N)]PF6 complexes are octahedral (the AA-H ligand binding involves N-amine and O-carboxylate), diamagnetic (low-spin d6, S=0) and present bands due to electronic transitions in the visible region. 1H, 13C{1H} and 31P{1H} NMR spectra of the complexes indicate the presence of C2 symmetry, and the identification of diastereoisomers. In vitro cytotoxicity assays of the compounds and cisplatin were carried out using MDA-MB-231 (human breast) tumor cell line and a non-tumor breast cell line (MCF-10A). Most complexes present promising results with IC50 values comparable with the reference drug cisplatin and high selectivity indexes were found for the complexes containing L-Trp. The binding of two Ru-precursors of the type [RuCl2(dppb)(NN)] (N-N=4'-MeObipy or 4'-Mebipy) to the blood transporter protein human serum albumin (HSA) was evaluated by fluorescence and circular dichroism spectroscopy. Both complexes bind HSA, probably in the hydrophobic pocket near Trp214, and the Ru-complex containing 4'-MeObipy shows higher affinity for HSA than the 4'-Mebipy one.
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Affiliation(s)
- Edjane R Dos Santos
- Departamento de Química, Universidade Federal de São Carlos, C.P. 676, CEP 13565-905 São Carlos, (SP), Brazil.
| | - Angelica E Graminha
- Departamento de Química, Universidade Federal de São Carlos, C.P. 676, CEP 13565-905 São Carlos, (SP), Brazil
| | - Mario S Schultz
- Núcleo em Ecologia e Desenvolvimento Sócio Ambiental de Macaé, Universidade Federal do Rio de Janeiro - Campus Macaé, CEP 27910-970 Macaé, RJ, Brazil
| | - Isabel Correia
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Heloisa S Selistre-de-Araújo
- Departamento de Ciências Fisiológicas, Universidade Federal de São Carlos, C.P. 676, CEP 13565-905 São Carlos, SP, Brazil
| | - Rodrigo S Corrêa
- Universidade Federal de Ouro Preto, Campos Morro do Cruzeiro, CEP 35.400-000 Ouro Preto, MG, Brazil
| | - Javier Ellena
- Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, CEP 13560-970 São Carlos, SP, Brazil
| | - Elisângela de Paula S Lacerda
- Laboratório de Genética Molecular e Citogenética, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - João Costa Pessoa
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Alzir A Batista
- Departamento de Química, Universidade Federal de São Carlos, C.P. 676, CEP 13565-905 São Carlos, (SP), Brazil
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16
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Ryder AG, Stedmon CA, Harrit N, Bro R. Calibration, standardization, and quantitative analysis of multidimensional fluorescence (MDF) measurements on complex mixtures (IUPAC Technical Report). PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractThis IUPAC Technical Report describes and compares the currently applied methods for the calibration and standardization of multi-dimensional fluorescence (MDF) spectroscopy data as well as recommendations on the correct use of chemometric methods for MDF data analysis. The paper starts with a brief description of the measurement principles for the most important MDF techniques and a short introduction to the most important applications. Recommendations are provided for instrument calibration, sample preparation and handling, and data collection, as well as the proper use of chemometric data analysis methods.
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Affiliation(s)
- Alan G. Ryder
- Nanoscale Biophotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Ireland
| | - Colin A. Stedmon
- National Institute for Aquatic Resources, Technical University of Denmark, DK-2800, Kgs.Lyngby, Denmark
| | - Niels Harrit
- Nanoscience Center, H. C. Ørsted Institute, Universitetsparken 5, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Rasmus Bro
- Department Food Science, Faculty of Life Sciences, University Copenhagen, DK-1958, Frederiksberg, Denmark
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17
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Biophysical and In Silico Studies of the Interaction between the Anti-Viral Agents Acyclovir and Penciclovir, and Human Serum Albumin. Molecules 2017; 22:molecules22111906. [PMID: 29113080 PMCID: PMC6150291 DOI: 10.3390/molecules22111906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Acyclovir (ACV) and penciclovir (PNV) have been commonly used during the last few decades as potent antiviral agents, especially for the treatment of herpes virus infections. In the present research their binding properties with human serum albumin (HSA) were studied using different advanced spectroscopic and in-silico methods. The interactions between ACV/PNV and HSA at the three investigated temperatures revealed a static type of binding. Extraction of the thermodynamic parameters of the ACV-HSA and PNV-HSA systems from the measured spectrofluorimetric data demonstrated spontaneous interactions with an enthalpy change (∆H0) of −1.79 ± 0.29 and −4.47 ± 0.51 kJ·mol−1 for ACV and PNV, respectively. The entropy change (∆S0) of 79.40 ± 0.95 and 69.95 ± 1.69 J·mol−1·K−1 for ACV and PNV, respectively, hence supported a potential contribution of electrostatic binding forces to the ACV-HSA and PNV-HSA systems. Putative binding of ACV/PNV to HSA, using previously reported site markers, showed that ACV/PNV were bound to HSA within subdomains IIA and IIIA (Sudlow sites I and II). Further confirmation was obtained through molecular docking studies of ACV-HSA and PNV-HSA binding, which confirmed the binding site of ACV/PNV with the most stable configurations of ACV/PNV within the HSA. These ACV/PNV conformers were shown to have free energies of −25.61 and −22.01 kJ·mol−1 for ACV within the HSA sites I and II and −22.97 and −26.53 kJ·mol−1 for PNV in HSA sites I and II, with hydrogen bonding and electrostatic forces being the main binding forces in such conformers.
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18
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Soysa HSM, Schulte A, Suginta W. Functional analysis of an unusual porin-like channel that imports chitin for alternative carbon metabolism in Escherichia coli. J Biol Chem 2017; 292:19328-19337. [PMID: 28972167 DOI: 10.1074/jbc.m117.812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli have the genetic potential to use chitin as a carbon source in the absence of glucose, importing it via the chitin-uptake channel EcChiP for processing by the glucosamine catabolic pathway. The chip gene is usually not expressed when E. coli are grown on glucose-enriched nutrients, providing a general regulatory mechanism for the pathway. EcChiP is unusual in that it is homologous to porins and monomeric instead of trimeric, the typical form of sugar-specific channels, making it unclear how this channel operates. We recently reported that EcChiP could form a stable channel in lipid membranes and that the channel is specific for chitooligosaccharides. This report describes the biophysical nature of sugar-channel interactions and the kinetics of sugar association and dissociation. Titrating EcChiP with chitohexaose resulted in protein fluorescence enhancement in a concentration-dependent manner, yielding a binding constant of 2.9 × 105 m-1, consistent with the value of 2.5 × 105 m-1 obtained from isothermal titration microcalorimetry. Analysis of the integrated heat change suggested that the binding process was endothermic and driven by entropy. Single-channel recordings confirmed the voltage dependence of the penetration of chitohexaose molecules into and their release from EcChiP. Once inside the pore, the sugar release rate (koff) from the affinity site increased with elevated voltage, regardless of the side of sugar addition. Our findings revealed distinct thermodynamic and kinetic features of the activity of sugar-specific EcChiP and advance our knowledge of the physiological possibility of chitin utilization by non-chitinolytic bacteria.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and
| | - Albert Schulte
- the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and .,the Center of Excellence in Advanced Functional Materials, Suranaree University of Technology Nakhon Ratchasima 30000, Thailand and
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19
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Bakou M, Hille K, Kracklauer M, Spanopoulou A, Frost CV, Malideli E, Yan LM, Caporale A, Zacharias M, Kapurniotu A. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly. J Biol Chem 2017; 292:14587-14602. [PMID: 28684415 DOI: 10.1074/jbc.m117.774893] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 07/02/2017] [Indexed: 12/28/2022] Open
Abstract
The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions.
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Affiliation(s)
- Maria Bakou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Kathleen Hille
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Michael Kracklauer
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Anna Spanopoulou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Christina V Frost
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Eleni Malideli
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Li-Mei Yan
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Andrea Caporale
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Martin Zacharias
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Aphrodite Kapurniotu
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
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20
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Kang F, Wang Q, Shou W, Collins CD, Gao Y. Alkali-earth metal bridges formed in biofilm matrices regulate the uptake of fluoroquinolone antibiotics and protect against bacterial apoptosis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:112-123. [PMID: 27638458 DOI: 10.1016/j.envpol.2016.09.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/06/2016] [Accepted: 09/11/2016] [Indexed: 06/06/2023]
Abstract
Bacterially extracellular biofilms play a critical role in relieving toxicity of fluoroquinolone antibiotic (FQA) pollutants, yet it is unclear whether antibiotic attack may be defused by a bacterial one-two punch strategy associated with metal-reinforced detoxification efficiency. Our findings help to assign functions to specific structural features of biofilms, as they strongly imply a molecularly regulated mechanism by which freely accessed alkali-earth metals in natural waters affect the cellular uptake of FQAs at the water-biofilm interface. Specifically, formation of alkali-earth-metal (Ca2+ or Mg2+) bridge between modeling ciprofloxacin and biofilms of Escherichia coli regulates the trans-biofilm transport rate of FQAs towards cells (135-nm-thick biofilm). As the addition of Ca2+ and Mg2+ (0-3.5 mmol/L, CIP: 1.25 μmol/L), the transport rates were reduced to 52.4% and 63.0%, respectively. Computational chemistry analysis further demonstrated a deprotonated carboxyl in the tryptophan residues of biofilms acted as a major bridge site, of which one side is a metal and the other is a metal girder jointly connected to the carboxyl and carbonyl of a FQA. The bacterial growth rate depends on the bridging energy at anchoring site, which underlines the environmental importance of metal bridge formed in biofilm matrices in bacterially antibiotic resistance.
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Affiliation(s)
- Fuxing Kang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Qian Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiangsu 210008, China
| | - Weijun Shou
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China
| | - Chris D Collins
- Soil Research Centre, University of Reading, Whiteknights, Reading RG6 6DW, UK
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Jiangsu 210095, China.
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21
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Gijsbers A, Nishigaki T, Sánchez-Puig N. Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions. J Vis Exp 2016. [PMID: 27805607 DOI: 10.3791/54640] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Protein-protein interactions play an essential role in the function of a living organism. Once an interaction has been identified and validated it is necessary to characterize it at the structural and mechanistic level. Several biochemical and biophysical methods exist for such purpose. Among them, fluorescence anisotropy is a powerful technique particularly used when the fluorescence intensity of a fluorophore-labeled protein remains constant upon protein-protein interaction. In this technique, a fluorophore-labeled protein is excited with vertically polarized light of an appropriate wavelength that selectively excites a subset of the fluorophores according to their relative orientation with the incoming beam. The resulting emission also has a directionality whose relationship in the vertical and horizontal planes defines anisotropy (r) as follows: r=(IVV-IVH)/(IVV+2IVH), where IVV and IVH are the fluorescence intensities of the vertical and horizontal components, respectively. Fluorescence anisotropy is sensitive to the rotational diffusion of a fluorophore, namely the apparent molecular size of a fluorophore attached to a protein, which is altered upon protein-protein interaction. In the present text, the use of fluorescence anisotropy as a tool to study protein-protein interactions was exemplified to address the binding between the protein mutated in the Shwachman-Diamond Syndrome (SBDS) and the Elongation factor like-1 GTPase (EFL1). Conventionally, labeling of a protein with a fluorophore is carried out on the thiol groups (cysteine) or in the amino groups (the N-terminal amine or lysine) of the protein. However, SBDS possesses several cysteines and lysines that did not allow site directed labeling of it. As an alternative technique, the dye 4',5'-bis(1,3,2 dithioarsolan-2-yl) fluorescein was used to specifically label a tetracysteine motif, Cys-Cys-Pro-Gly-Cys-Cys, genetically engineered in the C-terminus of the recombinant SBDS protein. Fitting of the experimental data provided quantitative and mechanistic information on the binding mode between these proteins.
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Affiliation(s)
- Abril Gijsbers
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México
| | - Takuya Nishigaki
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México;
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22
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Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
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23
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Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development. Appl Environ Microbiol 2016; 82:4133-4144. [PMID: 27208139 DOI: 10.1128/aem.00606-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The remarkable metal resistance of many microorganisms is related to the presence of multiple metal resistance operons. Pseudomonas putida KT2440 can be considered a model for these microorganisms since its arsenic resistance is due to the action of proteins encoded by the two paralogous arsenic resistance operons ARS1 and ARS2. Both operons contain the genes encoding the transcriptional regulators ArsR1 and ArsR2 that control operon expression. We show here that purified ArsR1 and ArsR2 bind the trivalent salt of arsenic (arsenite) with similar affinities (~30 μM), whereas no binding is observed for the pentavalent salt (arsenate). Furthermore, trivalent salts of bismuth and antimony showed binding to both paralogues. The positions of cysteines, found to bind arsenic in other homologues, indicate that ArsR1 and ArsR2 employ different modes of arsenite recognition. Both paralogues are dimeric and possess significant thermal stability. Both proteins were used to construct whole-cell, lacZ-based biosensors. Whereas responses to bismuth were negligible, significant responses were observed for arsenite, arsenate, and antimony. Biosensors based on the P. putida arsB1 arsB2 arsenic efflux pump double mutant were significantly more sensitive than biosensors based on the wild-type strain. This sensitivity enhancement by pump mutation may be a convenient strategy for the construction of other biosensors. A frequent limitation found for other arsenic biosensors was their elevated background signal and interference by inorganic phosphate. The constructed biosensors show no interference by inorganic phosphate, are characterized by a very low background signal, and were found to be suitable to analyze environmental samples. IMPORTANCE Arsenic is at the top of the priority list of hazardous compounds issued by the U.S. Agency for Toxic Substances and Disease. The reason for the stunning arsenic resistance of many microorganisms is the existence of paralogous arsenic resistance operons. Pseudomonas putida KT2440 is a model organism for such bacteria, and their duplicated ars operons and in particular their ArsR transcription regulators have been studied in depth by in vivo approaches. Here we present an analysis of both purified ArsR paralogues by different biophysical techniques, and data obtained provide valuable insight into their structure and function. Particularly insightful was the comparison of ArsR effector profiles determined by in vitro and in vivo experimentation. We also report the use of both paralogues to construct robust and highly sensitive arsenic biosensors. Our finding that the deletion of both arsenic efflux pumps significantly increases biosensor sensitivity is of general relevance in the biosensor field.
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24
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Tian Z, Liu J, Zhang Y. Structural insights into Cydia pomonella pheromone binding protein 2 mediated prediction of potentially active semiochemicals. Sci Rep 2016; 6:22336. [PMID: 26928635 PMCID: PMC4772377 DOI: 10.1038/srep22336] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/08/2016] [Indexed: 01/24/2023] Open
Abstract
Given the advantages of behavioral disruption application in pest control and the damage of Cydia pomonella, due progresses have not been made in searching active semiochemicals for codling moth. In this research, 31 candidate semiochemicals were ranked for their binding potential to Cydia pomonella pheromone binding protein 2 (CpomPBP2) by simulated docking, and this sorted result was confirmed by competitive binding assay. This high predicting accuracy of virtual screening led to the construction of a rapid and viable method for semiochemicals searching. By reference to binding mode analyses, hydrogen bond and hydrophobic interaction were suggested to be two key factors in determining ligand affinity, so is the length of molecule chain. So it is concluded that semiochemicals of appropriate chain length with hydroxyl group or carbonyl group at one head tended to be favored by CpomPBP2. Residues involved in binding with each ligand were pointed out as well, which were verified by computational alanine scanning mutagenesis. Progress made in the present study helps establish an efficient method for predicting potentially active compounds and prepares for the application of high-throughput virtual screening in searching semiochemicals by taking insights into binding mode analyses.
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Affiliation(s)
- Zhen Tian
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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25
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Chen J, van Dongen MA, Merzel RL, Dougherty CA, Orr BG, Kanduluru AK, Low PS, Marsh ENG, Banaszak Holl MM. Substrate-Triggered Exosite Binding: Synergistic Dendrimer/Folic Acid Action for Achieving Specific, Tight-Binding to Folate Binding Protein. Biomacromolecules 2016; 17:922-7. [PMID: 26815158 DOI: 10.1021/acs.biomac.5b01586] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polymer-ligand conjugates are designed to bind proteins for applications as drugs, imaging agents, and transport scaffolds. In this work, we demonstrate a folic acid (FA)-triggered exosite binding of a generation five poly(amidoamine) (G5 PAMAM) dendrimer scaffold to bovine folate binding protein (bFBP). The protein exosite is a secondary binding site on the protein surface, separate from the FA binding pocket, to which the dendrimer binds. Exosite binding is required to achieve the greatly enhanced binding constants and protein structural change observed in this study. The G5Ac-COG-FA1.0 conjugate bound tightly to bFBP, was not displaced by a 28-fold excess of FA, and quenched roughly 80% of the initial fluorescence. Two-step binding kinetics were measured using the intrinsic fluorescence of the FBP tryptophan residues to give a KD in the low nanomolar range for formation of the initial G5Ac-COG-FA1.0/FBP* complex, and a slow conversion to the tight complex formed between the dendrimer and the FBP exosite. The extent of quenching was sensitive to the choice of FA-dendrimer linker chemistry. Direct amide conjugation of FA to G5-PAMAM resulted in roughly 50% fluorescence quenching of the FBP. The G5Ac-COG-FA, which has a longer linker containing a 1,2,3-triazole ring, exhibited an ∼80% fluorescence quenching. The binding of the G5Ac-COG-FA1.0 conjugate was compared to poly(ethylene glycol) (PEG) conjugates of FA (PEGn-FA). PEG2k-FA had a binding strength similar to that of FA, whereas other PEG conjugates with higher molecular weight showed weaker binding. However, no PEG conjugates gave an increased degree of total fluorescence quenching.
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Affiliation(s)
| | | | | | | | | | - Ananda Kumar Kanduluru
- Department of Chemistry and Center for Drug Discovery, Purdue University , West Lafayette, Indiana 47907, United States
| | - Philip S Low
- Department of Chemistry and Center for Drug Discovery, Purdue University , West Lafayette, Indiana 47907, United States
| | - E Neil G Marsh
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Mark M Banaszak Holl
- Macromolecular Science and Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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26
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Funke A, Dickerhoff J, Weisz K. Towards the Development of Structure-Selective G-Quadruplex-Binding Indolo[3,2-b
]quinolines. Chemistry 2016; 22:3170-81. [DOI: 10.1002/chem.201504416] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Andrea Funke
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Klaus Weisz
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
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27
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Bartoccini F, Bartolucci S, Mari M, Piersanti G. A simple, modular synthesis of C4-substituted tryptophan derivatives. Org Biomol Chem 2016; 14:10095-10100. [DOI: 10.1039/c6ob01791f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A straightforward, rapid, versatile, regio- and chemoselective approach for the synthesis of C4-substituted tryptophan derivatives is reported.
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Affiliation(s)
- F. Bartoccini
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - S. Bartolucci
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - M. Mari
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
| | - G. Piersanti
- Department of Biomolecular Sciences
- University of Urbino “Carlo Bo”
- 61029 Urbino
- Italy
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28
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Pazos E, Mascareñas JL, Vázquez ME. Identification of Cyclin A Binders with a Fluorescent Peptide Sensor. Methods Mol Biol 2015; 1336:67-83. [PMID: 26231709 DOI: 10.1007/978-1-4939-2926-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A peptide sensor that integrates the 4-dimethylaminophthalimide (4-DMAP) fluorophore in a short cyclin A binding sequence displays a large fluorescence emission increase upon interacting with the cyclin A Binding Groove (CBG). Competitive displacement assays of this probe allow the straightforward identification of peptides that interact with the CBG, which could potentially block the recognition of CDK/cyclin A kinase substrates.
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Affiliation(s)
- Elena Pazos
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, C/ Jenaro de la Fuente s/n, Campus Vida, 15782, Santiago de Compostela, Spain
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29
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Rad B, Haxton TK, Shon A, Shin SH, Whitelam S, Ajo-Franklin CM. Ion-specific control of the self-assembly dynamics of a nanostructured protein lattice. ACS NANO 2015; 9:180-90. [PMID: 25494454 PMCID: PMC4310639 DOI: 10.1021/nn502992x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/10/2014] [Indexed: 05/22/2023]
Abstract
Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca(2+). These diagrams revealed a localized region of optimum yield of nanosheets at intermediate Ca(2+) concentration. Replacement of Mg(2+) or Ba(2+) for Ca(2+) indicates that Ca(2+) acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca(2+) bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. Our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.
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Affiliation(s)
- Behzad Rad
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Thomas K. Haxton
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Albert Shon
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720-1462, United States
| | - Seong-Ho Shin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemistry, UC Berkeley, Berkeley, California 94720-1460, United States
| | - Stephen Whitelam
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Caroline M. Ajo-Franklin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Address correspondence to
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30
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Feldmann EA, Galletto R. The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes. Biochemistry 2014; 53:7471-83. [PMID: 25382181 PMCID: PMC4263426 DOI: 10.1021/bi501049b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Saccharomyces cerevisiae repressor-activator protein
1 (Rap1) is an essential protein involved in multiple steps of DNA
regulation, as an activator in transcription, as a repressor at silencer
elements, and as a major component of the shelterin-like complex at
telomeres. All the known functions of Rap1 require the known high-affinity
and specific interaction of the DNA-binding domain with its recognition
sequences. In this work, we focus on the interaction of the DNA-binding
domain of Rap1 (Rap1DBD) with double-stranded DNA substrates.
Unexpectedly, we found that while Rap1DBD forms a high-affinity
1:1 complex with its DNA recognition site, it can also form lower-affinity
complexes with higher stoichiometries on DNA. These lower-affinity
interactions are independent of the presence of the recognition sequence,
and we propose they originate from the ability of Rap1DBD to bind to DNA in two different binding modes. In one high-affinity
binding mode, Rap1DBD likely binds in the conformation
observed in the available crystal structures. In the other alternative
lower-affinity binding mode, we propose that a single Myb-like domain
of the Rap1DBD makes interactions with DNA, allowing for
more than one protein molecule to bind to the DNA substrates. Our
findings suggest that the Rap1DBD does not simply target
the protein to its recognition sequence but rather it might be a possible
point of regulation.
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Affiliation(s)
- Erik A Feldmann
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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31
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New family of fluorogenic azacrown probes with identical cavity size but different electronic environment outside the macrocycle: effects on sensitivity of Cu2+ detection. J INCL PHENOM MACRO 2014. [DOI: 10.1007/s10847-014-0453-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Xue J, Ray R, Singer D, Böhme D, Burz DS, Rai V, Hoffmann R, Shekhtman A. The receptor for advanced glycation end products (RAGE) specifically recognizes methylglyoxal-derived AGEs. Biochemistry 2014; 53:3327-35. [PMID: 24824951 PMCID: PMC4038343 DOI: 10.1021/bi500046t] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diabetes-induced hyperglycemia increases the extracellular concentration of methylglyoxal. Methylglyoxal-derived hydroimidazolones (MG-H) form advanced glycation end products (AGEs) that accumulate in the serum of diabetic patients. The binding of hydroimidozolones to the receptor for AGEs (RAGE) results in long-term complications of diabetes typified by vascular and neuronal injury. Here we show that binding of methylglyoxal-modified albumin to RAGE results in signal transduction. Chemically synthesized peptides containing hydroimidozolones bind specifically to the V domain of RAGE with nanomolar affinity. The solution structure of an MG-H1-V domain complex revealed that the hydroimidazolone moiety forms multiple contacts with a positively charged surface on the V domain. The high affinity and specificity of hydroimidozolones binding to the V domain of RAGE suggest that they are the primary AGE structures that give rise to AGEs-RAGE pathologies.
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Affiliation(s)
- Jing Xue
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
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33
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Xu Q, Lu Y, Jing L, Cai L, Zhu X, Xie J, Hu X. Specific binding and inhibition of 6-benzylaminopurine to catalase: multiple spectroscopic methods combined with molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 123:327-335. [PMID: 24412785 DOI: 10.1016/j.saa.2013.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/05/2013] [Accepted: 12/05/2013] [Indexed: 06/03/2023]
Abstract
6-Benzylaminopurine (6-BA) is a kind of cytokinin which could regulate the activities of the antioxidant defense system of plants. In this work, its interaction with and inhibition of beef liver catalase have been systematically investigated using spectroscopic, isothermal titration calorimetric and molecular docking methods under physiological conditions. The fluorescence quenching of beef liver catalase (BLC) by 6-BA is due to the formation of 6-BA-BLC complex. Hydrogen bonds and van der Waals interactions play major roles in stabilizing the complex. The Stern-Volmer quenching constant, binding constant, the corresponding thermodynamic parameters and binding numbers were measured. The results of UV-vis absorption, three-dimensional fluorescence, synchronous fluorescence and circular dichroism spectroscopic results demonstrate that the binding of 6-BA results in the micro-environment change around tyrosine (Tyr) and tryptophan (Trp) residues of BLC. The BLC-mediated conversion of H2O2 to H2O and O2, in the presence and absence of 6-BA, was also studied. Lineweaver-Burk plot indicates a noncompetitive type of inhibition. Molecular docking study was used to find the binding sites.
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Affiliation(s)
- Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
| | - Yanni Lu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Longyun Jing
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Lijuan Cai
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Xinfeng Zhu
- College of Information Technology, Yangzhou University, Yangzhou 225127, China
| | - Ju Xie
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Xiaoya Hu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
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34
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Petersson EJ, Goldberg JM, Wissner RF. On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability. Phys Chem Chem Phys 2014; 16:6827-37. [PMID: 24598971 DOI: 10.1039/c3cp55525a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our laboratory has developed thioamide analogs of the natural amino acids as minimally-perturbing fluorescence quenching probes that can be placed at many locations in a protein sequence. We have shown that the mechanism of quenching can be either Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), depending on the identity of the donor fluorophore. Furthermore, we have shown that one can use a combination of semi-synthetic methods to label full-sized proteins with fluorophore-thioamide pairs. These probes can be used to study protein-protein interactions, protein folding or misfolding, and proteolysis.
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Affiliation(s)
- E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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35
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Makhlynets O, Boal AK, Rhodes DV, Kitten T, Rosenzweig AC, Stubbe J. Streptococcus sanguinis class Ib ribonucleotide reductase: high activity with both iron and manganese cofactors and structural insights. J Biol Chem 2013; 289:6259-72. [PMID: 24381172 DOI: 10.1074/jbc.m113.533554] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptococcus sanguinis is a causative agent of infective endocarditis. Deletion of SsaB, a manganese transporter, drastically reduces S. sanguinis virulence. Many pathogenic organisms require class Ib ribonucleotide reductase (RNR) to catalyze the conversion of nucleotides to deoxynucleotides under aerobic conditions, and recent studies demonstrate that this enzyme uses a dimanganese-tyrosyl radical (Mn(III)2-Y(•)) cofactor in vivo. The proteins required for S. sanguinis ribonucleotide reduction (NrdE and NrdF, α and β subunits of RNR; NrdH and TrxR, a glutaredoxin-like thioredoxin and a thioredoxin reductase; and NrdI, a flavodoxin essential for assembly of the RNR metallo-cofactor) have been identified and characterized. Apo-NrdF with Fe(II) and O2 can self-assemble a diferric-tyrosyl radical (Fe(III)2-Y(•)) cofactor (1.2 Y(•)/β2) and with the help of NrdI can assemble a Mn(III)2-Y(•) cofactor (0.9 Y(•)/β2). The activity of RNR with its endogenous reductants, NrdH and TrxR, is 5,000 and 1,500 units/mg for the Mn- and Fe-NrdFs (Fe-loaded NrdF), respectively. X-ray structures of S. sanguinis NrdIox and Mn(II)2-NrdF are reported and provide a possible rationale for the weak affinity (2.9 μM) between them. These streptococcal proteins form a structurally distinct subclass relative to other Ib proteins with unique features likely important in cluster assembly, including a long and negatively charged loop near the NrdI flavin and a bulky residue (Thr) at a constriction in the oxidant channel to the NrdI interface. These studies set the stage for identifying the active form of S. sanguinis class Ib RNR in an animal model for infective endocarditis and establishing whether the manganese requirement for pathogenesis is associated with RNR.
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36
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Li T, Lucius AL. Examination of the polypeptide substrate specificity for Escherichia coli ClpA. Biochemistry 2013; 52:4941-54. [PMID: 23773038 DOI: 10.1021/bi400178q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzyme-catalyzed protein unfolding is essential for a large array of biological functions, including microtubule severing, membrane fusion, morphogenesis and trafficking of endosomes, protein disaggregation, and ATP-dependent proteolysis. These enzymes are all members of the ATPases associated with various cellular activity (AAA+) superfamily of proteins. Escherichia coli ClpA is a hexameric ring ATPase responsible for enzyme-catalyzed protein unfolding and translocation of a polypeptide chain into the central cavity of the tetradecameric E. coli ClpP serine protease for proteolytic degradation. Further, ClpA also uses its protein unfolding activity to catalyze protein remodeling reactions in the absence of ClpP. ClpA recognizes and binds a variety of protein tags displayed on proteins targeted for degradation. In addition, ClpA binds unstructured or poorly structured proteins containing no specific tag sequence. Despite this, a quantitative description of the relative binding affinities for these different substrates is not available. Here we show that ClpA binds to the 11-amino acid SsrA tag with an affinity of 200 ± 30 nM. However, when the SsrA sequence is incorporated at the carboxy terminus of a 30-50-amino acid substrate exhibiting little secondary structure, the affinity constant decreases to 3-5 nM. These results indicate that additional contacts beyond the SsrA sequence are required for maximal binding affinity. Moreover, ClpA binds to various lengths of the intrinsically unstructured protein, α-casein, with an affinity of ∼30 nM. Thus, ClpA does exhibit modest specificity for SsrA when incorporated into an unstructured protein. Moreover, incorporating these results with the known structural information suggests that SsrA makes direct contact with the domain 2 loop in the axial channel and additional substrate length is required for additional contacts within domain 1.
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Affiliation(s)
- Tao Li
- Department of Chemistry, The University of Alabama at Birmingham , 1530 3rd Avenue South, Birmingham, Alabama 35294-1240, United States
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Sánchez MI, Vázquez O, Vázquez ME, Mascareñas JL. Sequence-selective DNA recognition with peptide-bisbenzamidine conjugates. Chemistry 2013; 19:9923-9. [PMID: 23780839 DOI: 10.1002/chem.201300519] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 12/15/2022]
Abstract
Transcription factors (TFs) are specialized proteins that play a key role in the regulation of genetic expression. Their mechanism of action involves the interaction with specific DNA sequences, which usually takes place through specialized domains of the protein. However, achieving an efficient binding usually requires the presence of the full protein. This is the case for bZIP and zinc finger TF families, which cannot interact with their target sites when the DNA binding fragments are presented as isolated monomers. Herein it is demonstrated that the DNA binding of these monomeric peptides can be restored when conjugated to aza-bisbenzamidines, which are readily accessible molecules that interact with A/T-rich sites by insertion into their minor groove. Importantly, the fluorogenic properties of the aza-benzamidine unit provide details of the DNA interaction that are eluded in electrophoresis mobility shift assays (EMSA). The hybrids based on the GCN4 bZIP protein preferentially bind to composite sequences containing tandem bisbenzamidine-GCN4 binding sites (TCAT⋅AAATT). Fluorescence reverse titrations show an interesting multiphasic profile consistent with the formation of competitive nonspecific complexes at low DNA/peptide ratios. On the other hand, the conjugate with the DNA binding domain of the zinc finger protein GAGA binds with high affinity (KD≈12 nM) and specificity to a composite AATTT⋅GAGA sequence containing both the bisbenzamidine and the TF consensus binding sites.
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Affiliation(s)
- Mateo I Sánchez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Perspicace S, Rufer AC, Thoma R, Mueller F, Hennig M, Ceccarelli S, Schulz-Gasch T, Seelig J. Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein. FEBS Open Bio 2013; 3:204-11. [PMID: 23772395 PMCID: PMC3668529 DOI: 10.1016/j.fob.2013.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 11/22/2022] Open
Abstract
Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of KD = 2–20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery. A first description of inhibitors that are specific for the CoA binding site of CPT-2. Distinct thermodynamic footprints are observed for site-specific inhibitors of CPT-2. Thermodynamic characterization of the CPT-2 active site correlates with structural data.
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Affiliation(s)
- Samantha Perspicace
- Division of Biophysical Chemistry, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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39
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Cotruvo JA, Stich TA, Britt RD, Stubbe J. Mechanism of assembly of the dimanganese-tyrosyl radical cofactor of class Ib ribonucleotide reductase: enzymatic generation of superoxide is required for tyrosine oxidation via a Mn(III)Mn(IV) intermediate. J Am Chem Soc 2013; 135:4027-39. [PMID: 23402532 DOI: 10.1021/ja312457t] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) utilize radical chemistry to reduce nucleotides to deoxynucleotides in all organisms. In the class Ia and Ib RNRs, this reaction requires a stable tyrosyl radical (Y(•)) generated by oxidation of a reduced dinuclear metal cluster. The Fe(III)2-Y(•) cofactor in the NrdB subunit of the class Ia RNRs can be generated by self-assembly from Fe(II)2-NrdB, O2, and a reducing equivalent. By contrast, the structurally homologous class Ib enzymes require a Mn(III)2-Y(•) cofactor in their NrdF subunit. Mn(II)2-NrdF does not react with O2, but it binds the reduced form of a conserved flavodoxin-like protein, NrdIhq, which, in the presence of O2, reacts to form the Mn(III)2-Y(•) cofactor. Here we investigate the mechanism of assembly of the Mn(III)2-Y(•) cofactor in Bacillus subtilis NrdF. Cluster assembly from Mn(II)2-NrdF, NrdI(hq), and O2 has been studied by stopped flow absorption and rapid freeze quench EPR spectroscopies. The results support a mechanism in which NrdI(hq) reduces O2 to O2(•-) (40-48 s(-1), 0.6 mM O2), the O2(•-) channels to and reacts with Mn(II)2-NrdF to form a Mn(III)Mn(IV) intermediate (2.2 ± 0.4 s(-1)), and the Mn(III)Mn(IV) species oxidizes tyrosine to Y(•) (0.08-0.15 s(-1)). Controlled production of O2(•-) by NrdIhq during class Ib RNR cofactor assembly both circumvents the unreactivity of the Mn(II)2 cluster with O2 and satisfies the requirement for an "extra" reducing equivalent in Y(•) generation.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Kozlov AG, Galletto R, Lohman TM. SSB-DNA binding monitored by fluorescence intensity and anisotropy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 922:55-83. [PMID: 22976177 DOI: 10.1007/978-1-62703-032-8_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fluorescence methods have proven to be extremely useful tools for quantitative studies of the equilibria and kinetics of protein-DNA interactions. If the protein contains tryptophan (Trp), as is often the case, and there is a change in intrinsic Trp fluorescence of the protein, one can use this change in signal (quenching/enhancement) to monitor binding. One can also attach an extrinsic fluorophore to either the protein or the DNA and monitor binding due to a change in fluorescence intensity or a change in fluorescence anisotropy. Such equilibrium studies can provide important quantitative information on stoichiometries (occluded site size, number of binding sites) and energetics (affinities and cooperativities) of the interactions. This information is needed to understand the mechanisms of protein-DNA interactions. A critical aspect of such approaches for systems that have non-unity stoichiometries (e.g., a protein that binds multiple ligands) is knowledge of the relationship between the change in fluorescence signal (intensity or anisotropy) and the average extent of binding. Here we describe procedures for using fluorescence approaches to examine the stoichiometries and equilibrium binding affinities of Escherichia coli single-stranded DNA-binding protein (SSB) and Deinococcus radiodurans SSB with long polymeric ssDNA to determine an occluded site size. We also provide examples of studies of SSB binding to shorter oligonucleotides to demonstrate analysis and fitting of the data to an appropriate model (monitoring fluorescence intensity or anisotropy) to obtain quantitative estimates of equilibrium binding parameters. We emphasize that the solution conditions (especially salt concentration and type) can influence not only the binding affinity, but also the mode by which an SSB oligomer binds ssDNA.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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41
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Moroz YS, Binder W, Nygren P, Caputo GA, Korendovych IV. Painting proteins blue: β-(1-azulenyl)-L-alanine as a probe for studying protein-protein interactions. Chem Commun (Camb) 2013; 49:490-2. [PMID: 23207368 PMCID: PMC3547328 DOI: 10.1039/c2cc37550h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrated that β-(1-azulenyl)-L-alanine, a fluorescent pseudoisosteric analog of tryptophan, exhibits weak environmental dependence and thus allows for using weak intrinsic quenchers, such as methionines, to monitor protein-protein interactions while not perturbing them.
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Affiliation(s)
- Yurii S. Moroz
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Wolfgang Binder
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
- Department of Chemistry, Technical University of Graz, Graz, Austria
| | - Patrik Nygren
- Department of Hematology and Oncology, University of Pennsylvania Medical School, Philadelphia, PA 19014, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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Papaneophytou CP, Mettou AK, Rinotas V, Douni E, Kontopidis GA. Solvent Selection for Insoluble Ligands, a Challenge for Biological Assay Development: A TNF-α/SPD304 Study. ACS Med Chem Lett 2013; 4:137-41. [PMID: 24900576 DOI: 10.1021/ml300380h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 11/29/2012] [Indexed: 11/28/2022] Open
Abstract
Many active compounds may be excluded from biological assays due to their low aqueous solubility. In this study, a simple method for the determination of the solubility of compounds containing aromatic rings is proposed. In addition to DMSO, five organic solvents for screening experiments of TNF-α inhibitors were explored. DMSO and PEG3350 were the most suitable for both protein stability and ligand-binding experiments. In addition, glycerol is a promising solvent for the screening of other compounds for which it might provide acceptable solubilization, due to its strong tendency to preserve the protein. Moreover, a fluorescence binding assay was developed using the TNF-α/SPD304 system, and a K d of 5.36 ± 0.21 μM was determined. The results of this study could be used for the future screening of potential TNF-α inhibitors, while the protocols developed in this work could be applied to other proteins.
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Affiliation(s)
- Christos P. Papaneophytou
- The Centre for Research and Technology of Thessaly (CE.RE.TE.TH.),
3rd km Karditsa-Mitropolis, Karditsa 43100, Greece
| | - Anthi K. Mettou
- The Centre for Research and Technology of Thessaly (CE.RE.TE.TH.),
3rd km Karditsa-Mitropolis, Karditsa 43100, Greece
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100,
Greece
| | - Vagelis Rinotas
- Laboratory of Genetics,
Department
of Agricultural Biotechnology, Agricultural University of Athens, Athens 11855, Greece
- Biomedical Science Research Center 'Alexander Fleming', Vari 16672, Greece
| | - Eleni Douni
- Laboratory of Genetics,
Department
of Agricultural Biotechnology, Agricultural University of Athens, Athens 11855, Greece
- Biomedical Science Research Center 'Alexander Fleming', Vari 16672, Greece
| | - George A. Kontopidis
- The Centre for Research and Technology of Thessaly (CE.RE.TE.TH.),
3rd km Karditsa-Mitropolis, Karditsa 43100, Greece
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100,
Greece
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Kovermann M, Balbach J. Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein. Biophys Chem 2013; 171:16-23. [DOI: 10.1016/j.bpc.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 12/13/2022]
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Riechert-Krause F, Autenrieth K, Eick A, Weisz K. Spectroscopic and calorimetric studies on the binding of an indoloquinoline drug to parallel and antiparallel DNA triplexes. Biochemistry 2012; 52:41-52. [PMID: 23234257 DOI: 10.1021/bi301381h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
11-Phenyl-substituted indoloquinolines have been found to exhibit significant antiproliferative potency in cancer cells but to show only moderate affinity toward genomic double-helical DNA. In this study, parallel as well as antiparallel triple-helical DNA targets are employed to evaluate the triplex binding of these ligands. UV melting experiments with parallel triplexes indicate considerable interactions with the drug and a strong preference for TAT-rich triplexes in line with an increasing number of potential intercalation sites of similar binding strength between two TAT base triads. Via substitution of a singly charged aminoethylamine side chain by a longer and doubly charged bis(aminopropyl)amine substituent at the ligand, binding affinities increase and also start to exhibit long-range effects as indicated by a strong correlation between the binding affinity and the overall length of the TAT tract within the triplex stem. Compared to parallel triplexes, an antiparallel triplex with a GT-containing third strand constitutes a preferred target for the indoloquinoline drug. On the basis of pH-dependent titration experiments and corroborated by a Job analysis of continuous variation, binding of the drug to the GT triplex not only is strongly enhanced when the solution pH is lowered from 7 to 5 but also reveals a pH-dependent stoichiometry upon formation of the complex. Calorimetric data demonstrate that stronger binding of a protonated drug at acidic pH is associated with a more exothermic binding process. However, at pH 7 and 5, binding is enthalpically driven with additional favorable entropic contributions.
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Affiliation(s)
- Fanny Riechert-Krause
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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45
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Havlíková M, Huličiak M, Bazgier V, Berka K, Kubala M. Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:568-76. [PMID: 23142565 DOI: 10.1016/j.bbamem.2012.10.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/24/2012] [Accepted: 10/31/2012] [Indexed: 11/30/2022]
Abstract
Combination of fluorescence techniques and molecular docking was used to monitor interaction of Na,K-ATPase and its large cytoplasmic loop connecting fourth and fifth transmembrane helices (C45) with fluorone dyes (i.e. eosin Y, 5(6)-carboxyeosin, rose bengal, fluorescein, and erythrosine B). Our data suggested that there are at least two binding sites for all used fluorone dyes, except of 5(6)-carboxyeosin. The first binding site is located on C45 loop, and it is sensitive to the presence of nucleotide. The other site is located on the extracellular part of the enzyme, and it is sensitive to the presence of Na(+) or K(+) ions. The molecular docking revealed that in the open conformation of C45 loop (which is obtained in the presence of ATP) all used fluorone dyes occupy position directly inside the ATP-binding pocket, while in the closed conformation (i.e. in the absence of any ligand) they are located only near the ATP-binding site depending on their different sizes. On the extracellular part of the protein, the molecular docking predicts two possible binding sites with similar binding energy near Asp897(α) or Gln69(β). The former was identified as a part of interaction site between α- and β-subunits, the latter is in contact with conserved FXYD sequence of the γ-subunit. Our findings provide structural explanation for numerous older studies, which were performed with fluorone dyes before the high-resolution structures were known. Further, fluorone dyes seem to be good probes for monitoring of intersubunit interactions influenced by Na(+) and K(+) binding.
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Affiliation(s)
- Marika Havlíková
- Department of Biophysics, Faculty of Science, Palacký University in Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
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46
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Mayr F, Schütz A, Döge N, Heinemann U. The Lin28 cold-shock domain remodels pre-let-7 microRNA. Nucleic Acids Res 2012; 40:7492-506. [PMID: 22570413 PMCID: PMC3424542 DOI: 10.1093/nar/gks355] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The RNA-binding protein Lin28 regulates the processing of a developmentally important group of microRNAs, the let-7 family. Lin28 blocks the biogenesis of let-7 in embryonic stem cells and thereby prevents differentiation. It was shown that both RNA-binding domains (RBDs) of this protein, the cold-shock domain (CSD) and the zinc-knuckle domain (ZKD) are indispensable for pri- or pre-let-7 binding and blocking its maturation. Here, we systematically examined the nucleic acid-binding preferences of the Lin28 RBDs and determined the crystal structure of the Lin28 CSD in the absence and presence of nucleic acids. Both RNA-binding domains bind to single-stranded nucleic acids with the ZKD mediating specific binding to a conserved GGAG motif and the CSD showing only limited sequence specificity. However, only the isolated Lin28 CSD, but not the ZKD, can bind with a reasonable affinity to pre-let-7 and thus is able to remodel the terminal loop of pre-let-7 including the Dicer cleavage site. Further mutagenesis studies reveal that the Lin28 CSD induces a conformational change in the terminal loop of pre-let-7 and thereby facilitates a subsequent specific binding of the Lin28 ZKD to the conserved GGAG motif.
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Affiliation(s)
- Florian Mayr
- Crystallography, Max-Delbrück Center for Molecular Medicine, Robert-Rössle Straße 10, 13125 Berlin, Germany
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47
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Zhao H, Berger AJ, Brown PH, Kumar J, Balbo A, May CA, Casillas E, Laue TM, Patterson GH, Mayer ML, Schuck P. Analysis of high-affinity assembly for AMPA receptor amino-terminal domains. J Gen Physiol 2012; 139:371-88. [PMID: 22508847 PMCID: PMC3343374 DOI: 10.1085/jgp.201210770] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 03/27/2012] [Indexed: 01/06/2023] Open
Abstract
Analytical ultracentrifugation (AUC) and steady-state fluorescence anisotropy were used to measure the equilibrium dissociation constant (Kd) for formation of dimers by the amino-terminal domains (ATDs) of the GluA2 and GluA3 subtypes of AMPA receptor. Previous reports on GluA2 dimerization differed in their estimate of the monomer-dimer Kd by a 2,400-fold range, with no consensus on whether the ATD forms tetramers in solution. We find by sedimentation velocity (SV) analysis performed using absorbance detection a narrow range of monomer-dimer Kd values for GluA2, from 5 to 11 nM for six independent experiments, with no detectable formation of tetramers and no effect of glycosylation or the polypeptide linker connecting the ATD and ligand-binding domains; for GluA3, the monomer-dimer Kd was 5.6 µM, again with no detectable tetramer formation. For sedimentation equilibrium (SE) experiments, a wide range of Kd values was obtained for GluA2, from 13 to 284 nM, whereas for GluA3, the Kd of 3.1 µM was less than twofold different from the SV value. Analysis of cell contents after the ∼1-week centrifuge run by silver-stained gels revealed low molecular weight GluA2 breakdown products. Simulated data for SE runs demonstrate that the apparent Kd for GluA2 varies with the extent of proteolysis, leading to artificially high Kd values. SV experiments with fluorescence detection for GluA2 labeled with 5,6-carboxyfluorescein, and fluorescence anisotropy measurements for GluA2 labeled with DyLight405, yielded Kd values of 5 and 11 nM, consistent with those from SV with absorbance detection. However, the sedimentation coefficients measured by AUC using absorbance and fluorescence systems were strikingly different, and for the latter are not consistent with hydrodynamic protein models. Thus, for unknown reasons, the concentration dependence of sedimentation coefficients obtained with fluorescence detection SV may be unreliable, limiting the usefulness of this technique for quantitative analysis.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Anthony J. Berger
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Patrick H. Brown
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Janesh Kumar
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Andrea Balbo
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, NH 03824
| | - Ernesto Casillas
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, NH 03824
| | - George H. Patterson
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Mark L. Mayer
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Peter Schuck
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
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48
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Štefanić Z, Narczyk M, Mikleušević G, Wielgus-Kutrowska B, Bzowska A, Luić M. New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A. FEBS Lett 2012; 586:967-71. [PMID: 22569248 DOI: 10.1016/j.febslet.2012.02.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/20/2012] [Accepted: 02/23/2012] [Indexed: 11/18/2022]
Abstract
Purine nucleoside phosphorylase (PNP) from Escherichia coli is a homohexamer that catalyses the phosphorolytic cleavage of the glycosidic bond of purine nucleosides. The first crystal structure of the ternary complex of this enzyme (with a phosphate ion and formycin A), which is biased by neither the presence of an inhibitor nor sulfate as a precipitant, is presented. The structure reveals, in some active sites, an unexpected and never before observed binding site for phosphate and exhibits a stoichiometry of two phosphate molecules per enzyme subunit. Moreover, in these active sites, the phosphate and nucleoside molecules are found not to be in direct contact. Rather, they are bridged by three water molecules that occupy the "standard" phosphate binding site.
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Affiliation(s)
- Zoran Štefanić
- Rudjer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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49
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Tanaka T, Mega R, Kim K, Shinkai A, Masui R, Kuramitsu S, Nakagawa N. A non-cold-inducible cold shock protein homolog mainly contributes to translational control under optimal growth conditions. FEBS J 2012; 279:1014-29. [PMID: 22251463 DOI: 10.1111/j.1742-4658.2012.08492.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) include both cold-induced and non-cold-induced proteins, contrary to their name. Cold-induced Csps are well studied; they function in cold acclimation by controlling transcription and translation. Some Csps have been reported to contribute to other cellular processes. However, the functions of non-cold-induced Csps under optimal growth conditions remain unknown. To elucidate these functions, we used transcriptome and proteome analyses as comprehensive approaches and have compared the outputs of wild-type and non-cold-induced Csp-deletion mutant cells. As a model organism, we selected Thermus thermophilus HB8 because it has only two csp genes (ttcsp1 and ttcsp2); ttCsp1 is the only non-cold-induced Csp. Surprisingly, the amount of transcripts and proteins upon deletion of the ttcsp1 gene was quite different. DNA microarray analysis revealed that the deletion of ttcsp1 did not affect the amount of transcripts, although the ttcsp1 gene was constantly expressed in the wild-type cell. Nonetheless, proteomic analysis revealed that the expression levels of many proteins were significantly altered when ttcsp1 was deleted. These results suggest that ttCsp1 functions in translation independent of transcription. Furthermore, ttCsp1 is involved in both the stimulation and inhibition of translation of specific proteins. Here, we have determined the crystal structure of ttCsp1 at 1.65 Å. This is the first report to present the structure of a non-cold-inducible cold shock protein. We also report the nucleotide binding affinity of ttCsp1. Finally, we discuss the functions of non-cold-induced Csps and propose how they modulate the levels of specific proteins to suit the prevailing environmental conditions.
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Affiliation(s)
- Toshiko Tanaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Japan
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Abbott DW, Boraston AB. Quantitative approaches to the analysis of carbohydrate-binding module function. Methods Enzymol 2012; 510:211-31. [PMID: 22608728 DOI: 10.1016/b978-0-12-415931-0.00011-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbohydrate-binding modules (CBMs) are important components of carbohydrate-active enzymes. Their primary functions are to assist in substrate turnover by targeting appended catalytic modules to substrate and concentrating appended catalytic modules on the surface of substrate. Presented here are four well-established methodologies for investigating and quantifying the CBM-polysaccharide binding relationship. These methods include: (1) the solid state depletion assay, (2) affinity gel electrophoresis, (3) UV difference and fluorescence spectroscopy, and (4) isothermal titration calorimetry. In addition, entropy-driven CBM-crystalline cellulose binding events and differential approaches to calculating stoichiometry with polyvalent polysaccharide ligands are also discussed.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Station, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
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