1
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Hou J, Zhang Q, Tian F, Liu F, Jiang J, Qin J, Wang H, Wang J, Chang S, Hu X. Structure changes of lignin and their effects on enzymatic hydrolysis for bioethanol production: a focus on lignin modification. J Biotechnol 2024; 393:61-73. [PMID: 39067576 DOI: 10.1016/j.jbiotec.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
Enzymatic hydrolysis contributes to obtaining fermentable sugars using pretreated lignocellulose materials for bioethanol generation. Unfortunately, the pretreatment of lignocellulose causes low substrate enzymatic hydrolysis, which is due to the structure changes of lignin to produce main phenolic by-products and non-productive cellulase adsorption. It is reported that modified lignin enhances the speed of enzymatic hydrolysis through single means to decrease the negative effects of fermentation inhibitors or non-productive cellulase adsorption. However, a suitable modified lignin should be selected to simultaneously reduce the fermentation inhibitors concentration and non-productive cellulase adsorption for saving resources and maximizing the enzymatic hydrolysis productivity. Meanwhile, the adsorption micro-mechanisms of modified lignin with fermentation inhibitors and cellulase remain elusive. In this review, different pretreatment effects toward lignin structure, and their impacts on subsequent enzymatic hydrolysis are analyzed. The main modification methods for lignin are presented. Density functional theory is used to screen suitable modification methods for the simultaneous reduction of fermentation inhibitors and non-productive cellulase adsorption. Lignin-fermentation inhibitors and lignin-cellulase interaction mechanisms are discussed using different advanced analysis techniques. This article addresses the gap in previous reviews concerning the application of modified lignin in the enhancement of bioethanol production. For the first time, based on existing studies, this work posits the hypothesis of applying theoretical simulations to screen efficient modified lignin-based adsorbents, in order to achieve a dual optimization of the detoxification and saccharification processes. We aim to improve the integrated lignocellulose transformation procedure for the effective generation of cleaner bioethanol.
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Affiliation(s)
- Jinju Hou
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Qiuzhuo Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Fuxiang Tian
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Fuwen Liu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jingxian Jiang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jiaolong Qin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Huifeng Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jing Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Shufang Chang
- School of Materials Science and Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Xiaojun Hu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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2
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Kalabekova R, Quinn CM, Movellan KT, Gronenborn AM, Akke M, Polenova T. 19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3. Biochemistry 2024; 63:2207-2216. [PMID: 39008798 DOI: 10.1021/acs.biochem.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.
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Affiliation(s)
- Roza Kalabekova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kumar Tekwani Movellan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, Lund SE-22100, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
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3
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Lu B, Liao SM, Liang SJ, Li JX, Liu XH, Huang RB, Zhou GP. NMR Studies of the Interactions between Sialyllactoses and the Polysialytransferase Domain for Polysialylation Inhibition. Curr Issues Mol Biol 2024; 46:5682-5700. [PMID: 38921011 PMCID: PMC11201969 DOI: 10.3390/cimb46060340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/30/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
It is known that sialyllactose (SL) in mammalians is a major source of sialic acid (Sia), which can further form cytidine monophosphate sialic acid (CMP-Sia), and the final product is polysialic acid (polySia) using polysialyltransferases (polySTs) on the neural cell adhesion molecule (NCAM). This process is called NCAM polysialylation. The overexpression of polysialylation is strongly related to cancer cell migration, invasion, and metastasis. In order to inhibit the overexpression of polysialylation, in this study, SL was selected as an inhibitor to test whether polysialylation could be inhibited. Our results suggest that the interactions between the polysialyltransferase domain (PSTD) in polyST and CMP-Siaand the PSTD and polySia could be inhibited when the 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL) concentration is about 0.5 mM or 6'-SL and 3 mM, respectively. The results also show that SLs (particularly for 3'-SL) are the ideal inhibitors compared with another two inhibitors, low-molecular-weight heparin (LMWH) and cytidine monophosphate (CMP), because 3'-SL can not only be used to inhibit NCAM polysialylation, but is also one of the best supplements for infant formula and the gut health system.
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Affiliation(s)
- Bo Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
| | - Si-Ming Liao
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
| | - Shi-Jie Liang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
| | - Jian-Xiu Li
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
| | - Xue-Hui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
- Life Science and Technology College, Guangxi University, Nanning 530004, China
- Rocky Mount Life Science Institute, Rocky Mount, NC 27804, USA
| | - Guo-Ping Zhou
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China; (B.L.); (S.-M.L.); (S.-J.L.); (J.-X.L.)
- Rocky Mount Life Science Institute, Rocky Mount, NC 27804, USA
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4
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Kang SJ, Kim DH, Lee BJ. Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance. Biophys Chem 2024; 309:107228. [PMID: 38552402 DOI: 10.1016/j.bpc.2024.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.
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Affiliation(s)
- Su-Jin Kang
- College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Mastermeditech Ltd., Seoul 07793, Republic of Korea.
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5
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Stenström O, Diehl C, Modig K, Akke M. Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit. Proc Natl Acad Sci U S A 2024; 121:e2317747121. [PMID: 38527204 PMCID: PMC10998626 DOI: 10.1073/pnas.2317747121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-ligand complex formation is fundamental to biological function. A central question is whether proteins spontaneously adopt binding-competent conformations to which ligands bind conformational selection (CS) or whether ligands induce the binding-competent conformation induced fit (IF). Here, we resolve the CS and IF binding pathways by characterizing protein conformational dynamics over a wide range of ligand concentrations using NMR relaxation dispersion. We determined the relative flux through the two pathways using a four-state binding model that includes both CS and IF. Experiments conducted without ligand show that galectin-3 exchanges between the ground-state conformation and a high-energy conformation similar to the ligand-bound conformation, demonstrating that CS is a plausible pathway. Near-identical crystal structures of the apo and ligand-bound states suggest that the high-energy conformation in solution corresponds to the apo crystal structure. Stepwise additions of the ligand lactose induce progressive changes in the relaxation dispersions that we fit collectively to the four-state model, yielding all microscopic rate constants and binding affinities. The ligand affinity is higher for the bound-like conformation than for the ground state, as expected for CS. Nonetheless, the IF pathway contributes greater than 70% of the total flux even at low ligand concentrations. The higher flux through the IF pathway is explained by considerably higher rates of exchange between the two protein conformations in the ligand-associated state. Thus, the ligand acts to decrease the activation barrier between protein conformations in a manner reciprocal to enzymatic transition-state stabilization of reactions involving ligand transformation.
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Affiliation(s)
- Olof Stenström
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Carl Diehl
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Kristofer Modig
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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6
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Kara H, Axer A, Muskett FW, Bueno-Alejo CJ, Paschalis V, Taladriz-Sender A, Tubasum S, Vega MS, Zhao Z, Clark AW, Hudson AJ, Eperon IC, Burley GA, Dominguez C. 2'- 19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Front Mol Biosci 2024; 11:1325041. [PMID: 38419689 PMCID: PMC10899400 DOI: 10.3389/fmolb.2024.1325041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.
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Affiliation(s)
- Hesna Kara
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Alexander Axer
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Frederick W Muskett
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Carlos J Bueno-Alejo
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Vasileios Paschalis
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Sumera Tubasum
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Marina Santana Vega
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Zhengyun Zhao
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Alasdair W Clark
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J Hudson
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Ian C Eperon
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Glenn A Burley
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Cyril Dominguez
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
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7
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Kundu S. A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network. Sci Rep 2024; 14:3507. [PMID: 38347039 PMCID: PMC10861591 DOI: 10.1038/s41598-024-53231-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Metabolism results from enzymatic- and non-enzymatic interactions of several molecules, is easily parameterized with the dissociation constant and occurs via biochemical networks. The dissociation constant is an empirically determined parameter and cannot be used directly to investigate in silico models of biochemical networks. Here, we develop and present an algorithm to define, compute and assess the relevance of the probable dissociation constant for every reaction of a biochemical network. The reactants and reactions of this network are modelled by a stoichiometry number matrix. The algorithm computes the null space and then serially generates subspaces by combinatorially summing the spanning vectors that are non-trivial and unique. This is done until the terms of each row either monotonically diverge or form an alternating sequence whose terms can be partitioned into subsets with almost the same number of oppositely signed terms. For a selected null space-generated subspace the algorithm utilizes several statistical and mathematical descriptors to select and bin terms from each row into distinct outcome-specific subsets. The terms of each subset are summed, mapped to the real-valued open interval [Formula: see text] and used to populate a reaction-specific outcome vector. The p1-norm for this vector is then the probable dissociation constant for this reaction. These steps are continued until every reaction of a modelled network is unambiguously annotated. The assertions presented are complemented by computational studies of a biochemical network for aerobic glycolysis. The fundamental premise of this work is that every row of a null space-generated subspace is a valid reaction and can therefore, be modelled as a reaction-specific sequence vector with a dimension that corresponds to the cardinality of the subspace after excluding all trivial- and redundant-vectors. A major finding of this study is that the row-wise sum or the sum of the terms contained in each reaction-specific sequence vector is mapped unambiguously to a positive real number. This means that the probable dissociation constants, for all reactions, can be directly computed from the stoichiometry number matrix and are suitable indicators of outcome for every reaction of the modelled biochemical network. Additionally, we find that the unambiguous annotation for a biochemical network will require a minimum number of iterations and will determine computational complexity.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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8
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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9
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Hőgye F, Farkas LB, Balogh ÁK, Szilágyi L, Alnukari S, Bajza I, Borbás A, Fehér K, Illyés TZ, Timári I. Saturation Transfer Difference NMR and Molecular Docking Interaction Study of Aralkyl-Thiodigalactosides as Potential Inhibitors of the Human-Galectin-3 Protein. Int J Mol Sci 2024; 25:1742. [PMID: 38339036 PMCID: PMC10855533 DOI: 10.3390/ijms25031742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3'-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3'-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation-π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3.
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Affiliation(s)
- Fanni Hőgye
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - László Bence Farkas
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Álex Kálmán Balogh
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - László Szilágyi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - Samar Alnukari
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - István Bajza
- GlycOptim Kft., Egyetem tér 1, H-4032 Debrecen, Hungary;
| | - Anikó Borbás
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Krisztina Fehér
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
| | - Tünde Zita Illyés
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
| | - István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (F.H.); (L.B.F.); (L.S.)
- HUN-REN-UD Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (Á.K.B.); (S.A.); (A.B.); (K.F.)
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10
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Kundu S. ReDirection: an R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network. Front Mol Biosci 2023; 10:1206502. [PMID: 37942290 PMCID: PMC10628733 DOI: 10.3389/fmolb.2023.1206502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/14/2023] [Indexed: 11/10/2023] Open
Abstract
Biochemical networks integrate enzyme-mediated substrate conversions with non-enzymatic complex formation and disassembly to accomplish complex biochemical and physiological functions. The choice of parameters and constraints used in most of these studies is numerically motivated and network-specific. Although sound in theory, the outcomes that result depart significantly from the intracellular milieu and are less likely to retain relevance in a clinical setting. There is a need for a computational tool which is biochemically relevant, mathematically rigorous, and unbiased, and can ascribe functionality to and generate potentially testable hypotheses for a user-defined biochemical network. Here, we present "ReDirection," an R-package which computes the probable dissociation constant for every reaction of a biochemical network directly from a null space-generated subspace of the stoichiometry number matrix of the modeled network. "ReDirection" delineates this subspace by excluding all trivial and redundant or duplicate occurrences of non-trivial vectors, combinatorially summing the vectors that remain and verifying that the upper or lower bounds of the sequence of terms formed by each row of this subspace belong to the open real-valued intervals - ∞ , - 1 or 1 , ∞ or whether the number of terms that are differently signed are almost equal. "ReDirection" iterates these steps until these bounds are consistent and unambiguous for all reactions of the modeled biochemical network. Thereafter, "ReDirection" filters the terms from each row of this subspace, bins them to outcome-specific subsets, sums and maps this to an outcome-specific reaction vector, and computes the p1-norm, which is the probable dissociation constant for a reaction. "ReDirection" works on first principles, does not discriminate between enzymatic and non-enzymatic reactions, offers a biochemically relevant and mathematically rigorous environment to explore user-defined biochemical networks under baseline and perturbed conditions, and can be used to address empirically intractable biochemical problems. The utility and relevance of "ReDirection" are highlighted by numerical studies on stoichiometric number models of biochemical networks of galactose metabolism and heme and cholesterol biosynthesis. "ReDirection" is freely available and accessible from the comprehensive R archive network (CRAN) with the URL (https://cran.r-project.org/package=ReDirection).
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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11
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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12
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Plata M, Sharma M, Utz M, Werner JM. Fully Automated Characterization of Protein-Peptide Binding by Microfluidic 2D NMR. J Am Chem Soc 2023; 145:3204-3210. [PMID: 36716203 PMCID: PMC9912330 DOI: 10.1021/jacs.2c13052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We demonstrate an automated microfluidic nuclear magnetic resonance (NMR) system that quantitatively characterizes protein-ligand interactions without user intervention and with minimal sample needs through protein-detected heteronuclear 2D NMR spectroscopy. Quantitation of protein-ligand interactions is of fundamental importance to the understanding of signaling and other life processes. As is well-known, NMR provides rich information both on the thermodynamics of binding and on the binding site. However, the required titrations are laborious and tend to require large amounts of sample, which are not always available. The present work shows how the analytical power of NMR detection can be brought in line with the trend of miniaturization and automation in life science workflows.
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Affiliation(s)
- Marek Plata
- School
of Chemistry, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Manvendra Sharma
- School
of Chemistry, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Marcel Utz
- School
of Chemistry, University of Southampton, SouthamptonSO17 1BJ, United Kingdom,Email
for M.U.:
| | - Jörn M. Werner
- School
for Biological Sciences, University of Southampton, B85 Life Science Building, University
Rd, SouthamptonSO17 1BJ, United Kingdom,Email for J.M.W.:
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13
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Antifungal Combination Eye Drops for Fungal Keratitis Treatment. Pharmaceutics 2022; 15:pharmaceutics15010035. [PMID: 36678663 PMCID: PMC9866460 DOI: 10.3390/pharmaceutics15010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Fungal keratitis (FK) is a corneal mycotic infection that can lead to vision loss. Furthermore, the severity of FK is aggravated by the emergence of resistant fungal species. There is currently only one FDA-approved formulation for FK treatment forcing hospital pharmacy departments to reformulate intravenous drug preparations with unknown ocular bioavailability and toxicity. In the present study, natamycin/voriconazole formulations were developed and characterized to improve natamycin solubility, permanence, and safety. The solubility of natamycin was studied in the presence of two cyclodextrins: HPβCD and HPγCD. The HPβCD was chosen based on the solubility results. Natamycin/cyclodextrin (HPβCD) inclusion complexes characterization and a competition study between natamycin and voriconazole were conducted by NMR (Nuclear Magnetic Resonance). Based on these results, several eye drops with different polymer compositions were developed and subsequently characterized. Permeability studies suggested that the formulations improved the passage of natamycin through the cornea compared to the commercial formulation Natacyn®. The ocular safety of the formulations was determined by BCOP and HET-CAM. The antifungal activity assay demonstrated the ability of our formulations to inhibit the in vitro growth of different fungal species. All these results concluded that the formulations developed in the present study could significantly improve the treatment of FK.
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14
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Březina V, Hanyková L, Velychkivska N, Hill JP, Labuta J. NMR lineshape analysis using analytical solutions of multi-state chemical exchange with applications to kinetics of host-guest systems. Sci Rep 2022; 12:17369. [PMID: 36253475 PMCID: PMC9576801 DOI: 10.1038/s41598-022-20136-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Nuclear magnetic resonance (NMR) lineshape analysis is a powerful tool for the study of chemical kinetics. Here we provide techniques for analysis of the relationship between experimentally observed spin kinetics (transitions between different environments [Formula: see text]) and corresponding chemical kinetics (transitions between distinct chemical species; e.g., free host and complexed host molecule). The advantages of using analytical solutions for two-, three- or generally N-state exchange lineshapes (without J-coupling) over the widely used numerical calculation for NMR spectral fitting are presented. Several aspects of exchange kinetics including the generalization of coalescence conditions in two-state exchange, the possibility of multiple processes between two states, and differences between equilibrium and steady-state modes are discussed. 'Reduced equivalent schemes' are introduced for spin kinetics containing fast-exchanging states, effectively reducing the number of exchanging states. The theoretical results have been used to analyze a host-guest system containing an oxoporphyrinogen complexed with camphorsulfonic acid and several other literature examples, including isomerization, protein kinetics, or enzymatic reactions. The theoretical treatment and experimental examples present an expansion of the systematic approach to rigorous analyses of systems with rich chemical kinetics through NMR lineshape analysis.
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Affiliation(s)
- Václav Březina
- grid.21941.3f0000 0001 0789 6880International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044 Japan ,grid.4491.80000 0004 1937 116XFaculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague 8, Czech Republic
| | - Lenka Hanyková
- grid.4491.80000 0004 1937 116XFaculty of Mathematics and Physics, Charles University, V Holešovičkách 2, 180 00 Prague 8, Czech Republic
| | - Nadiia Velychkivska
- grid.21941.3f0000 0001 0789 6880International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044 Japan ,grid.418095.10000 0001 1015 3316Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic
| | - Jonathan P. Hill
- grid.21941.3f0000 0001 0789 6880International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044 Japan
| | - Jan Labuta
- grid.21941.3f0000 0001 0789 6880International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044 Japan
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15
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Human Serine Racemase Weakly Binds the Third PDZ Domain of PSD-95. Int J Mol Sci 2022; 23:ijms23094959. [PMID: 35563349 PMCID: PMC9105370 DOI: 10.3390/ijms23094959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Human serine racemase (hSR) is a pyridoxal-5'-phosphate (PLP)-dependent dimer that catalyzes the formation of D-serine from L-serine, as well as the dehydration of both L- and D-serine to pyruvate and ammonia. As D-serine is a co-agonist of N-methyl-D-aspartate receptors (NMDARs), hSR is a key enzyme in glutamatergic neurotransmission. hSR activity is finely regulated by Mg2+, ATP, post-translational modifications, and the interaction with protein partners. In particular, the C-terminus of murine SR binds the third PDZ domain (PDZ3) of postsynaptic density protein 95 (PSD-95), a member of the membrane-associated guanylate kinase (MAGUK) family involved in the trafficking and localization of glutamate receptors. The structural details of the interaction and the stability of the complex have not been elucidated yet. We evaluated the binding of recombinant human PSD-95 PDZ3 to hSR by glutaraldehyde cross-linking, pull-down assays, isothermal titration calorimetry, nuclear magnetic resonance, and enzymatic assays. Overall, a weak interaction was observed, confirming the binding for the human orthologs but supporting the hypothesis that a third protein partner (i.e., stargazin) is required for the regulation of hSR activity by PSD-95 and to stabilize their interaction.
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16
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Paithankar H, Tarang GS, Parvez F, Marathe A, Joshi M, Chugh J. Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. Biophys J 2022; 121:1038-1055. [PMID: 35134335 PMCID: PMC8943759 DOI: 10.1016/j.bpj.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/25/2021] [Accepted: 02/03/2022] [Indexed: 11/02/2022] Open
Abstract
Many double-stranded RNA-binding domains (dsRBDs) interact with topologically distinct dsRNAs in biological pathways pivotal to viral replication, cancer causation, neurodegeneration, and so on. We hypothesized that the adaptability of dsRBDs is essential to target different dsRNA substrates. A model dsRBD and a few dsRNAs, slightly different in shape from each other, were used to test the systematic shape dependence of RNA on the dsRBD-binding using nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. NMR-based titrations showed a distinct binding pattern for the dsRBD with the topologically distinct dsRNAs. The line broadening upon RNA binding was observed to cluster in the residues lying in close proximity, thereby suggesting an RNA-induced conformational exchange in the dsRBD. Further, while the intrinsic microsecond dynamics observed in the apo-dsRBD were found to quench upon binding with the dsRNA, the microsecond dynamics got induced at residues spatially proximal to quench sites upon binding with the dsRNA. This apparent relay of conformational exchange suggests the significance of intrinsic dynamics to help adapt the dsRBD to target various dsRNA-shapes. The conformational pool visualized in MD simulations for the apo-dsRBD reported here has also been observed to sample the conformations seen previously for various dsRBDs in apo- and in dsRNA-bound state structures, further suggesting the conformational adaptability of the dsRBDs. These investigations provide a dynamic basis for the substrate promiscuity for dsRBD proteins.
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Affiliation(s)
- Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Guneet Singh Tarang
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Firdousi Parvez
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Aniket Marathe
- Bioinformatics Center, Savitrabai Phule Pune University, Pune, Maharashtra, India
| | - Manali Joshi
- Bioinformatics Center, Savitrabai Phule Pune University, Pune, Maharashtra, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India; Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India.
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17
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Oligosaccharide Presentation Modulates the Molecular Recognition of Glycolipids by Galectins on Membrane Surfaces. Pharmaceuticals (Basel) 2022; 15:ph15020145. [PMID: 35215258 PMCID: PMC8878398 DOI: 10.3390/ph15020145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Galectins are a family of glycan binding proteins that stand out for the wide range of biological phenomena in which they are involved. Most galectin functions are associated with their glycan binding capacities, which are generally well characterized at the oligosaccharide level, but not at the glycoprotein or glycolipid level. Glycolipids form the part of cell membranes where they can act as galectin cellular receptors. In this scenario, glycan presentation as well as the membrane chemical and structural features are expected to have a strong impact in these molecular association processes. Herein, liposomes were used as membrane mimicking scaffolds for the presentation of glycosphingolipids (GSLs) and to investigate their interaction with Galectin-3 and the N-domain of Galectin-8 (Gal8N). The binding towards GM3 and GM1 and their non-silaylated GSLs was compared to the binding to the free glycans, devoid of lipid. The analysis was carried out using a combination of NMR methods, membrane perturbation studies, and molecular modeling. Our results showed a different tendency of the two galectins in their binding capacities towards the glycans, depending on whether they were free oligosaccharides or as part of GSL inserted into a lipid bilayer, highlighting the significance of GSL glycan presentation on membranes in lectin binding.
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18
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Björklund E, du Rietz A, Lundström P. Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions. Protein Sci 2021; 31:301-307. [PMID: 34791737 PMCID: PMC8740844 DOI: 10.1002/pro.4240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022]
Abstract
We present PLIS, a publicly available, open‐source software for the determination of protein–ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.
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Affiliation(s)
- Emil Björklund
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Anna du Rietz
- Division of Molecular Surface Physics and Nanoscience, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Patrik Lundström
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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19
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Design and characterization of ellagic acid-loaded zein nanoparticles and their effect on the antioxidant and antibacterial activities. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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20
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Wickhorst PJ, Ihmels H, Paululat T. Studies on the Interactions of 3,11-Difluoro-6,8,13-trimethyl-8 H-quino[4,3,2- kl]acridinium and Insulin with the Quadruplex-Forming Oligonucleotide Sequence a2 from the Insulin-Linked Polymorphic Region. Molecules 2021; 26:molecules26216595. [PMID: 34771003 PMCID: PMC8587938 DOI: 10.3390/molecules26216595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, several quadruplex-DNA-forming sequences have been identified in the insulin-linked polymorphic region (ILPR), which is a guanine-rich oligonucleotide sequence in the promoter region of insulin. The formation of this non-canonical quadruplex DNA (G4-DNA) has been shown to be involved in the biological activity of the ILPR, specifically with regard to its interplay with insulin. In this context, this contribution reports on the investigation of the association of the quadruplex-forming ILPR sequence a2 with insulin as well as with the well-known G4-DNA ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium (1), also named RHPS4, by optical and NMR spectroscopy. CD- and NMR-spectroscopic measurements confirmed the preferential formation of an antiparallel quadruplex structure of a2 with four stacked guanine quartets. Furthermore, ligand 1 has high affinity toward a2 and binds by terminal π stacking to the G1-G11-G15-G25 quartet. In addition, the spectroscopic studies pointed to an association of insulin to the deoxyribose backbone of the loops of a2.
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21
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Welte H, Sinn P, Kovermann M. Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate. Chembiochem 2021; 22:2973-2980. [PMID: 34390111 PMCID: PMC8596521 DOI: 10.1002/cbic.202100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/30/2021] [Indexed: 11/12/2022]
Abstract
The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.
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Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Pia Sinn
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
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22
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Hirakawa T, Walinda E, Morimoto D, Sugase K. Rigorous analysis of the interaction between proteins and low water-solubility drugs by qNMR-aided NMR titration experiments. Phys Chem Chem Phys 2021; 23:21484-21488. [PMID: 34569579 DOI: 10.1039/d1cp03175a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Drugs are designed and validated based on physicochemical data on their interactions with target proteins. For low water-solubility drugs, however, quantitative analysis is practically impossible without accurate estimation of precipitation. Here we combined quantitative NMR with NMR titration experiments to rigorously quantify the interaction of the low water-solubility drug pimecrolimus with its target protein FKBP12. Notably, the dissociation constants estimated with and without consideration of precipitation differed by more than tenfold. Moreover, the method enabled us to quantitate the FKBP12-pimecrolimus interaction even under a crowded condition established using the protein crowder BSA. Notably, the FKBP12-pimecrolimus interaction was slightly hampered under the crowded environment, which is explained by transient association of BSA with the drug molecules. Collectively, the described method will contribute to both quantifying the binding properties of low water-solubility drugs and to elucidating the drug behavior in complex crowded solutions including living cells.
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Affiliation(s)
- Takuya Hirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
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23
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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24
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Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci 2021; 22:9128. [PMID: 34502039 PMCID: PMC8430952 DOI: 10.3390/ijms22179128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.
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Affiliation(s)
- Chiara M. Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kiera L. Malone
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Claudia Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Simon J. Holton
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Mátyás Gorjánácz
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jamie C. Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, CA 94720, USA;
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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25
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McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
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26
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Chruszcz M, Chew FT, Hoffmann‐Sommergruber K, Hurlburt BK, Mueller GA, Pomés A, Rouvinen J, Villalba M, Wöhrl BM, Breiteneder H. Allergens and their associated small molecule ligands-their dual role in sensitization. Allergy 2021; 76:2367-2382. [PMID: 33866585 PMCID: PMC8286345 DOI: 10.1111/all.14861] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023]
Abstract
Many allergens feature hydrophobic cavities that allow the binding of primarily hydrophobic small‐molecule ligands. Ligand‐binding specificities can be strict or promiscuous. Serum albumins from mammals and birds can assume multiple conformations that facilitate the binding of a broad spectrum of compounds. Pollen and plant food allergens of the family 10 of pathogenesis‐related proteins bind a variety of small molecules such as glycosylated flavonoid derivatives, flavonoids, cytokinins, and steroids in vitro. However, their natural ligand binding was reported to be highly specific. Insect and mammalian lipocalins transport odorants, pheromones, catecholamines, and fatty acids with a similar level of specificity, while the food allergen β‐lactoglobulin from cow's milk is notably more promiscuous. Non‐specific lipid transfer proteins from pollen and plant foods bind a wide variety of lipids, from phospholipids to fatty acids, as well as sterols and prostaglandin B2, aided by the high plasticity and flexibility displayed by their lipid‐binding cavities. Ligands increase the stability of allergens to thermal and/or proteolytic degradation. They can also act as immunomodulatory agents that favor a Th2 polarization. In summary, ligand‐binding allergens expose the immune system to a variety of biologically active compounds whose impact on the sensitization process has not been well studied thus far.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Chemistry and Biochemistry University of South Carolina Columbia SC USA
| | - Fook Tim Chew
- Department of Biological Sciences National University of Singapore Singapore
| | - Karin Hoffmann‐Sommergruber
- Division of Medical Biotechnology Department of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - Barry K. Hurlburt
- Agricultural Research Service Southern Regional Research Center US Department of Agriculture New Orleans LA USA
| | - Geoffrey A. Mueller
- National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park NC USA
| | - Anna Pomés
- Indoor Biotechnologies, Inc. Charlottesville VA USA
| | - Juha Rouvinen
- Department of Chemistry University of Eastern Finland Joensuu Finland
| | - Mayte Villalba
- Department of Biochemistry and Molecular Biology Universidad Complutense de Madrid Madrid Spain
| | | | - Heimo Breiteneder
- Division of Medical Biotechnology Department of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
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27
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Forero AM, Castellanos L, Sandoval-Hernández AG, Magalhães A, Tinoco LW, Lopez-Vallejo F, Ramos FA. Integration of NMR studies, computational predictions, and in vitro assays in the search of marine diterpenes with antitumor activity. Chem Biol Drug Des 2021; 98:507-521. [PMID: 34143939 DOI: 10.1111/cbdd.13907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/14/2021] [Accepted: 06/06/2021] [Indexed: 12/01/2022]
Abstract
Among the compounds of natural origin, diterpenes have proved useful as drugs for the treatment of cancer. Marine organisms, such as soft corals and algae, are a promising source of diterpenes, being a rich and unexplored source of cytotoxic agents. This study evaluated a library of 32 natural and semisynthetic marine diterpenes, including briarane, cembrane, and dolabellane nuclei, with the aim of determining their cytotoxicity against three human cancer cell lines (A549, MCF7, and PC3). The three most active compounds were submitted to a flow cytometry analysis in order to determine induction of apoptosis against the A549 cell line. An NMR analysis was conducted to determine and evaluate the interactions between active diterpenes and tubulin. These interactions were characterized by a computational study using molecular docking and MD simulations. With these results, two cembrane and one chlorinated briarane diterpenes were active against the three human cancer cell lines, induced apoptosis in the A549 cell line, and showed interactions with tubulin preferably at the taxane-binding site. This study is a starting point for the identification and optimization of the marine diterpenes selected for better antitumor activities. It also highlights the power of integrating NMR studies, computational predictions, and in vitro assays in the search for compounds with antitumor activity.
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Affiliation(s)
- Abel M Forero
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia.,Departamento de Farmacia, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Leonardo Castellanos
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Adrián G Sandoval-Hernández
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia.,Instituto de Genética Humana, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Alvicler Magalhães
- Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Instituto de Química, Avenida Horácio Macedo, Cidade Universitária, Rio de Janeiro, Brazil
| | - Luzineide W Tinoco
- Laboratório Multiusuário de Análises por RMN (LAMAR), Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabian Lopez-Vallejo
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
| | - Freddy A Ramos
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia - Sede Bogotá, Bogotá, Colombia
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28
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Duff MR, Redzic JS, Ryan LP, Paukovich N, Zhao R, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ. Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family. J Biochem 2021; 168:191-202. [PMID: 32246827 DOI: 10.1093/jb/mvaa039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/19/2020] [Indexed: 11/14/2022] Open
Abstract
Biliverdin reductase B (BLVRB) family members are general flavin reductases critical in maintaining cellular redox with recent findings revealing that BLVRB alone can dictate cellular fate. However, as opposed to most enzymes, the BLVRB family remains enigmatic with an evolutionarily changing active site and unknown structural and functional consequences. Here, we applied a multi-faceted approach that combines X-ray crystallography, NMR and kinetics methods to elucidate the structural and functional basis of the evolutionarily changing BLVRB active site. Using a panel of three BLVRB isoforms (human, lemur and hyrax) and multiple human BLVRB mutants, our studies reveal a novel evolutionary mechanism where coenzyme 'clamps' formed by arginine side chains at two co-evolving positions within the active site serve to slow coenzyme release (Positions 14 and 78). We find that coenzyme release is further slowed by the weaker binding substrate, resulting in relatively slow turnover numbers. However, different BLVRB active sites imposed by either evolution or mutagenesis exhibit a surprising inverse relationship between coenzyme release and substrate turnover that is independent of the faster chemical step of hydride transfer also measured here. Collectively, our studies have elucidated the role of the evolutionarily changing BLVRB active site that serves to modulate coenzyme release and has revealed that coenzyme release is coupled to substrate turnover.
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Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Lucas P Ryan
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Pratul Agarwal
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
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29
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García-Otero X, Díaz-Tomé V, Varela-Fernández R, Martín-Pastor M, González-Barcia M, Blanco-Méndez J, Mondelo-García C, Bermudez MA, Gonzalez F, Aguiar P, Fernández-Ferreiro A, Otero-Espinar FJ. Development and Characterization of a Tacrolimus/Hydroxypropyl-β-Cyclodextrin Eye Drop. Pharmaceutics 2021; 13:pharmaceutics13020149. [PMID: 33498753 PMCID: PMC7911614 DOI: 10.3390/pharmaceutics13020149] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 02/03/2023] Open
Abstract
Uveitis is a vision inflammatory disorder with a high prevalence in developing countries. Currently, marketed treatments remain limited and reformulation is usually performed to obtain a tacrolimus eye drop as a therapeutic alternative in corticosteroid-refractory eye disease. The aim of this work was to develop a mucoadhesive, non-toxic and stable topical ophthalmic formulation that can be safely prepared in hospital pharmacy departments. Four different ophthalmic formulations were prepared based on the tacrolimus/hydroxypropyl-β-cyclodextrin (HPβCD) inclusion complexes’ formation. Phase solubility diagrams, Nuclear Magnetic Resonance (NMR) and molecular modeling studies showed the formation of 1:1 and 1:2 tacrolimus/HPβCD inclusion complexes, being possible to obtain a 0.02% (w/v) tacrolimus concentration by using 40% (w/v) HPβCD aqueous solutions. Formulations also showed good ophthalmic properties in terms of pH, osmolality and safety. Stability studies proved these formulations to be stable for at least 3 months in refrigeration. Ex vivo bioadhesion and in vivo ocular permanence showed good mucoadhesive properties with higher ocular permanence compared to the reference pharmacy compounding used in clinical settings (t1/2 of 86.2 min for the eyedrop elaborated with 40% (w/v) HPβCD and Liquifilm® versus 46.3 min for the reference formulation). Thus, these novel eye drops present high potential as a safe alternative for uveitis treatment, as well as a versatile composition to include new drugs intended for topical ophthalmic administration.
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Affiliation(s)
- Xurxo García-Otero
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain; (X.G.-O.); (V.D.-T.); (R.V.-F.); (J.B.-M.)
- Molecular Imaging Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - Victoria Díaz-Tomé
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain; (X.G.-O.); (V.D.-T.); (R.V.-F.); (J.B.-M.)
- Clinical Pharmacology Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.G.-B.); (C.M.-G.)
| | - Rubén Varela-Fernández
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain; (X.G.-O.); (V.D.-T.); (R.V.-F.); (J.B.-M.)
- Clinical Neurosciences Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - Manuel Martín-Pastor
- Nuclear Magnetic Resonance Unit, Research Infrastructures Area, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
| | - Miguel González-Barcia
- Clinical Pharmacology Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.G.-B.); (C.M.-G.)
| | - José Blanco-Méndez
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain; (X.G.-O.); (V.D.-T.); (R.V.-F.); (J.B.-M.)
- Paraquasil Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - Cristina Mondelo-García
- Clinical Pharmacology Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.G.-B.); (C.M.-G.)
| | - Maria A. Bermudez
- Physiology Department–CIMUS, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
| | - Francisco Gonzalez
- Ophthalmology Department, Clinical University Hospital Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain;
- Department of Surgery and Medical-Surgical Specialties and CIMUS, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Pablo Aguiar
- Molecular Imaging Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
- Correspondence: (P.A.); (A.F.-F.); (F.J.O.-E.); Tel.: +34-881814878 (F.J.O.-E.)
| | - Anxo Fernández-Ferreiro
- Clinical Pharmacology Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (M.G.-B.); (C.M.-G.)
- Correspondence: (P.A.); (A.F.-F.); (F.J.O.-E.); Tel.: +34-881814878 (F.J.O.-E.)
| | - Francisco J. Otero-Espinar
- Pharmacology, Pharmacy and Pharmaceutical Technology Department, Faculty of Pharmacy, University of Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain; (X.G.-O.); (V.D.-T.); (R.V.-F.); (J.B.-M.)
- Paraquasil Group, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
- Correspondence: (P.A.); (A.F.-F.); (F.J.O.-E.); Tel.: +34-881814878 (F.J.O.-E.)
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30
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Abel S, Marchi M. Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11802-11818. [PMID: 33346653 DOI: 10.1021/acs.jpcb.0c08902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural studies of proteins and, in particular, integral membrane proteins (IMPs) using solution NMR spectroscopy approaches are challenging due to not only their inherent structural complexities but also the fact that they need to be solubilized in biomimetic environments (such as micelles), which enhances the slow molecular reorientation. To deal with these difficulties and increase the effective rate of molecular reorientation, the encapsulation of IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low-viscosity solvent has been proven to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMP structure and function is little known. To gain insight into these aspects, this article presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with anionic surfactant diacyl chain bis(2-ethylhexyl) sodium succinate (AOT) in pentane at a water-to-surfactant molar ratio (W0) of 6. The simulations were carried out with different protocols and starting conditions for a total of 2.4 μs and were compared with other MDs used with the gA channel inserted in models of the SDS micelle or the DMPC membrane. We show here that in the presence of AOT RMs the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-terminal parts of the gA are capped with two RMs and the rest of the dimer is protected from the oil solvent by the AOT acyl chains. In contrast, the MD simulations reveal that the AOT, Na+, and water formed two well-defined and elongated RMs attached to the C-terminal ends of the gA dimer, while the rest is in direct contact with the pentane. The initial β6.3 secondary structure of the gA is well conserved and filled with 6-9 waters, as in SDS micelles or the DMPC membrane. Finally, the water movement inside the gA is strongly affected by the presence of RMs at each extremity, and no passage of water molecules through the gA channel is observed even after a long simulation period, whereas the opposite was found for gA in SDS and DMPC.
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Affiliation(s)
- Stéphane Abel
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Massimo Marchi
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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31
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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32
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Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G. NMR in target driven drug discovery: why not? JOURNAL OF BIOMOLECULAR NMR 2020; 74:521-529. [PMID: 32901320 PMCID: PMC7683447 DOI: 10.1007/s10858-020-00343-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/17/2020] [Indexed: 05/09/2023]
Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
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Affiliation(s)
| | | | | | | | | | - Eiso Ab
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands
| | | | - Gerhard Müller
- Gotham GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany
| | - Gregg Siegal
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands.
- Amsterdam Institute of Molecular and Life Sciences, Free University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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Puig E, Tolchard J, Riera A, Carulla N. Somatostatin, an In Vivo Binder to Aβ Oligomers, Binds to βPFO Aβ(1-42) Tetramers. ACS Chem Neurosci 2020; 11:3358-3365. [PMID: 32915532 DOI: 10.1021/acschemneuro.0c00470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Somatostatin (SST14) is strongly related to Alzheimer's disease (AD), as its levels decline during aging, it regulates the proteolytic degradation of the amyloid beta peptide (Aβ), and it binds to Aβ oligomers in vivo. Recently, the 3D structure of a membrane-associated β-sheet pore-forming tetramer (βPFOAβ(1-42) tetramer) has been reported. Here, we show that SST14 binds selectively to the βPFOAβ(1-42) tetramer with a KD value of ∼40 μM without binding to monomeric Aβ(1-42). Specific NMR chemical shift perturbations, observed during titration of SST14, define a binding site in the βPFOAβ(1-42) tetramer and are in agreement with a 2:1 stoichiometry determined by both native mass spectroscopy and isothermal titration calorimetry. These results enabled us to perform driven docking and model the binding mode for the interaction. The present study provides additional evidence on the relation between SST14 and the amyloid cascade and positions the βPFOAβ(1-42) tetramer as a relevant aggregation form of Aβ and as a potential target for AD.
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Affiliation(s)
- Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - James Tolchard
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franqués 1, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- CBMN (UMR 5248), University of Bordeaux−CNRS−IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, Pessac 33600, France
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Garlick JM, Mapp AK. Selective Modulation of Dynamic Protein Complexes. Cell Chem Biol 2020; 27:986-997. [PMID: 32783965 PMCID: PMC7469457 DOI: 10.1016/j.chembiol.2020.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic proteins are prime candidates for chemical probe and drug discovery but difficult targets because they do not conform to classical rules of design and screening. Selectivity is pivotal for candidate probe molecules due to the extensive interaction network of these dynamic hubs. Recognition that the traditional rules of probe discovery are not necessarily applicable to dynamic proteins and their complexes, as well as technological advances in screening, have produced remarkable results in the last 2-4 years. Particularly notable are the improvements in target selectivity for small-molecule modulators of dynamic proteins, especially with techniques that increase the discovery likelihood of allosteric regulatory mechanisms. We focus on approaches to small-molecule screening that appear to be more suitable for highly dynamic targets and have the potential to streamline identification of selective modulators.
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Affiliation(s)
- Julie M Garlick
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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35
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Cass QB, Massolini G, Cardoso CL, Calleri E. Editorial: Advances in Bioanalytical Methods for Probing Ligand-Target Interactions. Front Chem 2020; 8:378. [PMID: 32500056 PMCID: PMC7242755 DOI: 10.3389/fchem.2020.00378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/09/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Quezia B Cass
- Departamento de Química, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - Carmen Lucia Cardoso
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Enrica Calleri
- Departamento de Química, Universidade Federal de São Carlos, São Carlos, Brazil
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Nishizawa M, Walinda E, Morimoto D, Sugase K. Pinpoint analysis of a protein in slow exchange using F 1F 2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis. JOURNAL OF BIOMOLECULAR NMR 2020; 74:205-211. [PMID: 32236785 DOI: 10.1007/s10858-020-00309-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
ZZ-exchange spectroscopy is widely used to study slow exchange processes in biomolecules, especially determination of exchange rates and assignment of minor peaks. However, if the exchange cross peaks overlap or the populations are skewed, kinetic analysis is hindered. In order to analyze slow exchange protein dynamics under such conditions, here we have developed a new method by combining ZZ-exchange and F1F2-selective NMR spectroscopy. We demonstrate the utility of this method by examining the monomer-dimer transition of the ubiquitin-associated domain of p62, successfully assigning the minor (monomeric) peaks and obtaining the exchange rates, which cannot be achieved by ZZ-exchange alone.
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Affiliation(s)
- Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-ku Yoshida Konoe-cho, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.
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37
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Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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38
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Purslow JA, Khatiwada B, Bayro MJ, Venditti V. NMR Methods for Structural Characterization of Protein-Protein Complexes. Front Mol Biosci 2020; 7:9. [PMID: 32047754 PMCID: PMC6997237 DOI: 10.3389/fmolb.2020.00009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/10/2020] [Indexed: 01/21/2023] Open
Abstract
Protein-protein interactions and the complexes thus formed are critical elements in a wide variety of cellular events that require an atomic-level description to understand them in detail. Such complexes typically constitute challenging systems to characterize and drive the development of innovative biophysical methods. NMR spectroscopy techniques can be applied to extract atomic resolution information on the binding interfaces, intermolecular affinity, and binding-induced conformational changes in protein-protein complexes formed in solution, in the cell membrane, and in large macromolecular assemblies. Here we discuss experimental techniques for the characterization of protein-protein complexes in both solution NMR and solid-state NMR spectroscopy. The approaches include solvent paramagnetic relaxation enhancement and chemical shift perturbations (CSPs) for the identification of binding interfaces, and the application of intermolecular nuclear Overhauser effect spectroscopy and residual dipolar couplings to obtain structural constraints of protein-protein complexes in solution. Complementary methods in solid-state NMR are described, with emphasis on the versatility provided by heteronuclear dipolar recoupling to extract intermolecular constraints in differentially labeled protein complexes. The methods described are of particular relevance to the analysis of membrane proteins, such as those involved in signal transduction pathways, since they can potentially be characterized by both solution and solid-state NMR techniques, and thus outline key developments in this frontier of structural biology.
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Affiliation(s)
- Jeffrey A Purslow
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | | | - Marvin J Bayro
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA, United States.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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Abstract
RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state but also on the energy cost associated with changing the RNA conformational distribution. Measuring these "conformational penalties" is, however, challenging because bound RNA conformations tend to have equilibrium populations in the absence of the binding partner that fall outside detection by conventional biophysical methods. In this study we employ as a model system HIV-1 TAR RNA and its interaction with the ligand argininamide (ARG), a mimic of TAR's cognate protein binding partner, the transactivator Tat. We use NMR chemical shift perturbations and relaxation dispersion in combination with Bayesian inference to develop a detailed thermodynamic model of coupled conformational change and ligand binding. Starting from a comprehensive 12-state model of the equilibrium, we estimate the energies of six distinct detectable thermodynamic states that are not accessible by currently available methods. Our approach identifies a minimum of four RNA intermediates that differ in terms of the TAR conformation and ARG occupancy. The dominant bound TAR conformation features two bound ARG ligands and has an equilibrium population in the absence of ARG that is below detection limit. Consequently, even though ARG binds to TAR with an apparent overall weak affinity (Kdapp ≈ 0.2 mM), it binds the prefolded conformation with a Kd in the nM range. Our results show that conformational penalties can be major determinants of RNA-ligand binding affinity as well as a source of binding cooperativity, with important implications for a predictive understanding of how RNA is recognized and for RNA-targeted drug discovery.
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Affiliation(s)
- Nicole I. Orlovsky
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G. Oas
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Sci Rep 2019; 9:16023. [PMID: 31690758 PMCID: PMC6831641 DOI: 10.1038/s41598-019-52451-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/14/2019] [Indexed: 11/08/2022] Open
Abstract
The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.
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41
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Dagil L, Troelsen KS, Bolt G, Thim L, Wu B, Zhao X, Tuddenham EGD, Nielsen TE, Tanner DA, Faber JH, Breinholt J, Rasmussen JE, Hansen DF. Interaction Between the a3 Region of Factor VIII and the TIL'E' Domains of the von Willebrand Factor. Biophys J 2019; 117:479-489. [PMID: 31349985 PMCID: PMC6697466 DOI: 10.1016/j.bpj.2019.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/19/2019] [Accepted: 07/08/2019] [Indexed: 01/25/2023] Open
Abstract
The von Willebrand factor (VWF) and coagulation factor VIII (FVIII) are intricately involved in hemostasis. A tight, noncovalent complex between VWF and FVIII prolongs the half-life of FVIII in plasma, and failure to form this complex leads to rapid clearance of FVIII and bleeding diatheses such as hemophilia A and von Willebrand disease (VWD) type 2N. High-resolution insight into the complex between VWF and FVIII has so far been strikingly lacking. This is particularly the case for the flexible a3 region of FVIII, which is imperative for high-affinity binding. Here, a structural and biophysical characterization of the interaction between VWF and FVIII is presented with focus on two of the domains that have been proven pivotal for mediating the interaction, namely the a3 region of FVIII and the TIL'E' domains of VWF. Binding between the FVIII a3 region and VWF TIL'E' was here observed using NMR spectroscopy, where chemical shift changes were localized to two β-sheet regions on the edge of TIL'E' upon FVIII a3 region binding. Isothermal titration calorimetry and NMR spectroscopy were used to characterize the interaction between FVIII and TIL'E' as well as mutants of TIL'E', which further highlights the importance of the β-sheet region of TIL'E' for high-affinity binding. Overall, the results presented provide new insight into the role the FVIII a3 region plays for complex formation between VWF and FVIII and the β-sheet region of TIL'E' is shown to be important for FVIII binding. Thus, the results pave the way for further high-resolution insights into this imperative complex.
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Affiliation(s)
- Lisbeth Dagil
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom; Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Kathrin S Troelsen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gert Bolt
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Lars Thim
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Bo Wu
- Novo Nordisk Research Center China, Beijing, China
| | - Xin Zhao
- Novo Nordisk Research Center China, Beijing, China
| | - Edward G D Tuddenham
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom; Katharine Dormandy, Haemophilia Centre and Thrombosis Unit, Royal Free Hospital NHS Trust, London, United Kingdom
| | | | - David A Tanner
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | | | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.
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42
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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43
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Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
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Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
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Tavares WDS, Martin-Pastor M, Tavares AG, Sousa FFO. Biopharmaceutical Activities Related to Ellagic Acid, Chitosan, and Zein and Their Improvement by Association. J Food Sci 2019; 83:2970-2975. [PMID: 30537014 DOI: 10.1111/1750-3841.14369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/21/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022]
Abstract
Ellagic acid (EA) has demonstrated several biological properties, such as antioxidant, antimicrobial, and enzymatic inhibition. Zein and chitosan (CHI) are natural polymers whose biological potential has also gained attention. Therefore, this paper aimed to evaluate the antimicrobial, antioxidant, anticollagenase, and antielastase properties of EA, zein, and chitosan isolated or in combination. The microdilution method was used to assess the minimum inhibitory and bactericide concentrations. The antioxidant activity was determined using the 2,2-diphenyl-1-picryl-hydrazila free radical scavenging method. The anticollagenase and antielastase activities were evaluated by specific colorimetric tests. EA has shown inhibitory activity against Staphylococcus aureus and Pseudomonas aeruginosa together with an antioxidant IC50 of 0.079 mg/mL. EA also showed significant collagenase and elastase inhibition. Zein has shown antimicrobial and antioxidant activities itself and enhanced sinergically the antioxidant activity and the antimicrobial activity against P. aeruginosa when combined with EA. CHI increased sinergically the inhibitory activity of EA against both bacterial strains, while showed itself an acceptable antimicrobial activity. 1 H saturation transfer-difference nuclear magnetic resonance experiment confirmed the formation of a complex between EA and zein that could be related with the improvement on its biological performance over the individual compounds, while no chemical interaction was detected between CHI and EA. PRACTICAL APPLICATION: The results reinforce the potential of ellagic acid in combination with zein and/or chitosan as an antimicrobial, antienzimatic, and antioxidant agent. Those findings reinforce the use of these substances, protecting this bioactive from degradation and/or improving the functional characteristics and biopharmaceutical properties.
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Affiliation(s)
- Walter de S Tavares
- Dept. of Biological Sciences and Health, Federal Univ. of Amapa, Rod. Juscelino Kubitschek, Km-02 - Jardim Marco Zero, Macapá-AP, 68903-419, Brazil
| | - Manuel Martin-Pastor
- Unidade de Resonancia Magnética, RIAIDT, CACTUS, Univ. of Santiago de Compostela, Santiago de Compostela, A Coruña, 15706, Spain
| | - Alberto G Tavares
- Dept. of Biological Sciences and Health, Federal Univ. of Amapa, Rod. Juscelino Kubitschek, Km-02 - Jardim Marco Zero, Macapá-AP, 68903-419, Brazil
| | - Francisco F O Sousa
- Dept. of Biological Sciences and Health, Federal Univ. of Amapa, Rod. Juscelino Kubitschek, Km-02 - Jardim Marco Zero, Macapá-AP, 68903-419, Brazil
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Walinda E, Morimoto D, Sugase K. Overview of Relaxation Dispersion NMR Spectroscopy to Study Protein Dynamics and Protein-Ligand Interactions. ACTA ACUST UNITED AC 2019; 92:e57. [PMID: 30040207 DOI: 10.1002/cpps.57] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins and nucleic acids are central to all biological processes. NMR spectroscopy has proven to be excellent for studying the dynamics of these macromolecules over various timescales. Relaxation rates and heteronuclear nuclear Overhauser-effect values can resolve motion on pico- to nanosecond timescales, residual dipolar couplings provide information on submicro- to millisecond timescales, and even slower dynamics over seconds to hours can be resolved by hydrogen-exchange experiments. Relaxation dispersion experiments are especially valuable because they resolve motion on micro- to millisecond timescales, encompassing biomolecular motions associated with ligand binding, enzymatic catalysis, and domain-domain opening. These experiments provide structural, kinetic, and thermodynamic information on "invisible" excited conformational states. Relaxation dispersion can be applied not only to single biomolecules but also to protein-ligand complexes to study the kinetics and thermodynamics of association and dissociation. We review recent developments in relaxation dispersion methodology, outline the R1ρ relaxation dispersion experiment, and discuss application to biomolecular interactions. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-Ku, Kyoto, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, Japan
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46
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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48
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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49
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Kim Y, Liu M, Hilty C. Determination of binding affinities using hyperpolarized NMR with simultaneous 4-channel detection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 295:80-86. [PMID: 30144688 PMCID: PMC6201311 DOI: 10.1016/j.jmr.2018.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 05/23/2023]
Abstract
Dissolution dynamic nuclear polarization (D-DNP) is a powerful technique to improve NMR sensitivity by a factor of thousands. Combining D-DNP with NMR-based screening enables to mitigate solubility or availability problems of ligands and target proteins in drug discovery as it can lower the concentration requirements into the sub-micromolar range. One of the challenges that D-DNP assisted NMR screening methods face for broad application, however, is a reduced throughput due to additional procedures and time required to create hyperpolarization. These requirements result in a delay of several tens of minutes in-between each NMR measurement. To solve this problem, we have developed a simultaneous 4-channel detection method for hyperpolarized 19F NMR, which can increase throughput fourfold by utilizing a purpose-built multiplexed NMR spectrometer and probe. With this system, the concentration-dependent binding interactions were observed for benzamidine and benzylamine with the serine protease trypsin. A T2 relaxation measurement of a hyperpolarized reporter ligand (TFBC; CF3C6H4CNHNH2), which competes for the same binding site on trypsin with the other ligands, was used. The hyperpolarized TFBC was mixed with trypsin and the ligand of interest, and injected into four flow cells inside the NMR probe. Across the set of four channels, a concentration gradient was created. From the simultaneously acquired relaxation datasets, it was possible to determine the dissociation constant (KD) of benzamidine and benzylamine without the requirement for individually optimizing experimental conditions for different affinities. A simulation showed that this 4-channel detection method applied to D-DNP NMR extends the screenable KD range to up to three orders of magnitude in a single experiment.
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Affiliation(s)
- Yaewon Kim
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | - Mengxiao Liu
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | - Christian Hilty
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA.
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Resolving biomolecular motion and interactions by R2 and R1ρ relaxation dispersion NMR. Methods 2018; 148:28-38. [DOI: 10.1016/j.ymeth.2018.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
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