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Shen H, Zhang C, Li S, Liang Y, Lee LT, Aggarwal N, Wun KS, Liu J, Nadarajan SP, Weng C, Ling H, Tay JK, Wang DY, Yao SQ, Hwang IY, Lee YS, Chang MW. Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy. Nat Commun 2024; 15:4343. [PMID: 38773197 PMCID: PMC11109227 DOI: 10.1038/s41467-024-48661-y] [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: 09/25/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Prodrugs have been explored as an alternative to conventional chemotherapy; however, their target specificity remains limited. The tumor microenvironment harbors a range of microorganisms that potentially serve as tumor-targeting vectors for delivering prodrugs. In this study, we harness bacteria-cancer interactions native to the tumor microbiome to achieve high target specificity for prodrug delivery. We identify an oral commensal strain of Lactobacillus plantarum with an intrinsic cancer-binding mechanism and engineer the strain to enable the surface loading of anticancer prodrugs, with nasopharyngeal carcinoma (NPC) as a model cancer. The engineered commensals show specific binding to NPC via OppA-mediated recognition of surface heparan sulfate, and the loaded prodrugs are activated by tumor-associated biosignals to release SN-38, a chemotherapy compound, near NPC. In vitro experiments demonstrate that the prodrug-loaded microbes significantly increase the potency of SN-38 against NPC cell lines, up to 10-fold. In a mouse xenograft model, intravenous injection of the engineered L. plantarum leads to bacterial colonization in NPC tumors and a 67% inhibition in tumor growth, enhancing the efficacy of SN-38 by 54%.
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Affiliation(s)
- Haosheng Shen
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Changyu Zhang
- Ningbo Institute of Dalian University of Technology, Ningbo, China
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Shengjie Li
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Li Ting Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Kwok Soon Wun
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jing Liu
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Saravanan Prabhu Nadarajan
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheng Weng
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Wilmar International Limited, Singapore, Singapore
| | - Joshua K Tay
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Food, Chemical and Biotechnology, Singapore Institute of Technology, Singapore, Singapore.
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- National Centre for Engineering Biology (NCEB), Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Pawloski W, Komiyama T, Kougentakis C, Majumdar A, Fushman D. Site-Specific Detection and Characterization of Ubiquitin Carbamylation. Biochemistry 2022; 61:712-721. [PMID: 35380792 PMCID: PMC9173829 DOI: 10.1021/acs.biochem.2c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physiological consequences of varying in vivo CO2 levels point to a general mechanism for CO2 to influence cellular homeostasis beyond regulating pH. Aside from a few instances where CO2 has been observed to cause post-translational protein modification, by forming long-lived carbamates, little is known about how transitory and ubiquitous carbamylation events could induce a physiological response. Ubiquitin is a versatile protein involved in a multitude of cellular signaling pathways as polymeric chains of various lengths formed through one of the seven lysines or N-terminal amine. Unique polyubiquitin (polyUb) compositions present recognition signals for specific ubiquitin-receptors which enables this one protein to be involved in many different cellular processes. Advances in proteomic methods have allowed the capture and identification of protein carbamates in vivo, and Ub was found carbamylated at lysines K48 and K33. This was shown to negatively regulate ubiquitin-mediated signaling by inhibiting polyUb chain formation. Here, we expand upon these observations by characterizing the carbamylation susceptibility for all Ub amines simultaneously. Using NMR methods which directly probe 15N resonances, we determined carbamylation rates under various environmental conditions and related them to the intrinsic pKas. Our results show that the relatively low pKas for half of the Ub amines are correlated with enhanced susceptibility to carbamylation under physiological conditions. Two of these carbamylated amines, not observed by chemical capture, appear to be physiologically relevant post-translational modifications. These findings point to a mechanism for varying the levels of CO2 due to intracellular localization, cellular stresses, and metabolism to affect certain polyUb-mediated signaling pathways.
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Affiliation(s)
- Westley Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Teppei Komiyama
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Christos Kougentakis
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
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Ryan EO, Jiang Z, Nguyen H, Wang X. Interactions of Pleiotrophin with a Structurally Defined Heparin Hexasaccharide. Biomolecules 2021; 12:biom12010050. [PMID: 35053198 PMCID: PMC8773689 DOI: 10.3390/biom12010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/21/2022] Open
Abstract
Pleiotrophin (PTN) is a potent cytokine that plays an important role in neural generation, angiogenesis, inflammation, and cancers. Its interactions with the polysaccharide glycosaminoglycan (GAG) are crucial to PTN’s biological activities. In this study, we investigated the interaction of selectively protonated PTN with the heparin hexasaccharide ΔUA2S-(GlcNS6S-IdoA2S)2-GlcNS6S using solution NMR. The use of a structurally defined oligosaccharide and selectively protonated PTN enabled us to obtain intermolecular contacts using unfiltered NOESY experiments, significantly increasing the amount of high-resolution structural information obtainable. Our data showed that PTN’s arginines, lysines, and tryptophans in the two structured domains have strong interactions with the 2-O-sulfated uronate protons in the heparin hexasaccharide. Consistent with the NMR data is the observation that 2-O-desulfation and N-desulfation/N-acetylation significantly decreased heparin hexasaccharides’ affinity for PTN, while 6-O-desulfation only modestly affected the interactions with PTN. These results allowed us to hypothesize that PTN has a preference for sulfate clusters centered on the GlcNS6S-IdoA2S disaccharide. Using these data and the fact that PTN domains mostly bind heparin hexasaccharides independently, models of the PTN-heparin complex were constructed.
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Affiliation(s)
| | | | | | - Xu Wang
- Correspondence: ; Tel.: +1-480-7278256
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Wu H, Kohler J. Photocrosslinking probes for capture of carbohydrate interactions. Curr Opin Chem Biol 2019; 53:173-182. [PMID: 31706134 DOI: 10.1016/j.cbpa.2019.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023]
Abstract
Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have been designed and applied to study the biological functions of glycans. This review will discuss recent advances in the development of novel photocrosslinking functional groups and the design of photocrosslinking probes to detect interactions mediated by glycolipids, peptidoglycan, and multivalent carbohydrate ligands. These probes have demonstrated the potential to address some of the major challenges in the study of glycan-mediated interactions in both model systems and in more complex biological settings.
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Affiliation(s)
- Han Wu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer Kohler
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA. http://
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Das EC, Dhawan S, Babu J, Anil Kumar PR, Kumary TV, Haridas V, Komath M. Self‐assembling polymeric dendritic peptide as functional osteogenic matrix for periodontal regeneration scaffolds—an in vitro study. J Periodontal Res 2019; 54:468-480. [DOI: 10.1111/jre.12647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/17/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Eva C. Das
- Biomedical Technology WingSree Chitra Tirunal Institute of Medical Sciences and Technology Thiruvananthapuram India
| | - Sameer Dhawan
- Department of ChemistryIndian Institute of Technology Delhi New Delhi India
| | - Jisha Babu
- Department of ChemistryIndian Institute of Technology Delhi New Delhi India
| | - PR Anil Kumar
- Biomedical Technology WingSree Chitra Tirunal Institute of Medical Sciences and Technology Thiruvananthapuram India
| | - Thrikkovil Variathu Kumary
- Biomedical Technology WingSree Chitra Tirunal Institute of Medical Sciences and Technology Thiruvananthapuram India
| | - V Haridas
- Department of ChemistryIndian Institute of Technology Delhi New Delhi India
| | - Manoj Komath
- Biomedical Technology WingSree Chitra Tirunal Institute of Medical Sciences and Technology Thiruvananthapuram India
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On the origin of proteins in human drusen: The meet, greet and stick hypothesis. Prog Retin Eye Res 2018; 70:55-84. [PMID: 30572124 DOI: 10.1016/j.preteyeres.2018.12.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022]
Abstract
Retinal drusen formation is not only a clinical hallmark for the development of age-related macular degeneration (AMD) but also for other disorders, such as Alzheimer's disease and renal diseases. The initiation and growth of drusen is poorly understood. Attention has focused on lipids and minerals, but relatively little is known about the origin of drusen-associated proteins and how they are retained in the space between the basal lamina of the retinal pigment epithelium and the inner collagenous layer space (sub-RPE-BL space). While some authors suggested that drusen proteins are mainly derived from cellular debris from processed photoreceptor outer segments and the RPE, others suggest a choroidal cell or blood origin. Here, we reviewed and supplemented the existing literature on the molecular composition of the retina/choroid complex, to gain a more complete understanding of the sources of proteins in drusen. These "drusenomics" studies showed that a considerable proportion of currently identified drusen proteins is uniquely originating from the blood. A smaller, but still large fraction of drusen proteins comes from both blood and/or RPE. Only a small proportion of drusen proteins is uniquely derived from the photoreceptors or choroid. We next evaluated how drusen components may "meet, greet and stick" to each other and/or to structures like hydroxyapatite spherules to form macroscopic deposits in the sub-RPE-BL space. Finally, we discuss implications of our findings with respect to the previously proposed homology between drusenogenesis in AMD and plaque formation in atherosclerosis.
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Nguyen D, Chen C, Pettitt BM, Iwahara J. NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics. Methods Enzymol 2018; 615:285-332. [PMID: 30638532 DOI: 10.1016/bs.mie.2018.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NMR spectroscopy is a powerful tool for studying protein dynamics. Conventionally, NMR studies on protein dynamics have probed motions of protein backbone NH, side-chain aromatic, and CH3 groups. Recently, there has been remarkable progress in NMR methodologies that can characterize motions of cationic groups in protein side chains. These NMR methods allow investigations of the dynamics of positively charged lysine (Lys) and arginine (Arg) side chains and their hydrogen bonds as well as their electrostatic interactions important for protein function. Here, describing various practical aspects, we provide an overview of the NMR methods for dynamics studies of Lys and Arg side chains. Some example data on protein-DNA complexes are shown. We will also explain how molecular dynamics (MD) simulations can facilitate the interpretation of the NMR data on these basic side chains. Studies combining NMR and MD have revealed the highly dynamic nature of short-range electrostatic interactions via ion pairs, especially those involving Lys side chains.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Chuanying Chen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States.
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Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy. Molecules 2018; 23:molecules23092314. [PMID: 30208595 PMCID: PMC6225283 DOI: 10.3390/molecules23092314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.
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9
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Yang Y, Denton H, Davies OR, Smith-Jackson K, Kerr H, Herbert AP, Barlow PN, Pickering MC, Marchbank KJ. An Engineered Complement Factor H Construct for Treatment of C3 Glomerulopathy. J Am Soc Nephrol 2018; 29:1649-1661. [PMID: 29588430 PMCID: PMC6054357 DOI: 10.1681/asn.2017091006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Background C3 glomerulopathy (C3G) is associated with dysregulation of the alternative pathway of complement activation, and treatment options for C3G remain limited. Complement factor H (FH) is a potent regulator of the alternative pathway and might offer a solution, but the mass and complexity of FH makes generation of full-length FH far from trivial. We previously generated a mini-FH construct, with FH short consensus repeats 1-5 linked to repeats 18-20 (FH1-5^18-20), that was effective in experimental C3G. However, the serum t1/2 of FH1-5^18-20 was significantly shorter than that of serum-purified FH.Methods We introduced the oligomerization domain of human FH-related protein 1 (denoted by R1-2) at the carboxy or amino terminus of human FH1-5^18-20 to generate two homodimeric mini-FH constructs (FHR1-2^1-5^18-20 and FH1-5^18-20^R1-2, respectively) in Chinese hamster ovary cells and tested these constructs using binding, fluid-phase, and erythrocyte lysis assays, followed by experiments in FH-deficient Cfh-/- mice.Results FHR1-2^1-5^18-20 and FH1-5^18-20^R1-2 homodimerized in solution and displayed avid binding profiles on clustered C3b surfaces, particularly FHR1-2^1-5^18-20 Each construct was >10-fold more effective than FH at inhibiting cell surface complement activity in vitro and restricted glomerular basement membrane C3 deposition in vivo significantly better than FH or FH1-5^18-20 FH1-5^18-20^R1-2 had a C3 breakdown fragment binding profile similar to that of FH, a >5-fold increase in serum t1/2 compared with that of FH1-5^18-20, and significantly better retention in the kidney than FH or FH1-5^18-20Conclusions FH1-5^18-20^R1-2 may have utility as a treatment option for C3G or other complement-mediated diseases.
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Affiliation(s)
- Yi Yang
- Institute of Cellular Medicine, Newcastle University and National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Harriet Denton
- Institute of Cellular Medicine, Newcastle University and National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kate Smith-Jackson
- Institute of Cellular Medicine, Newcastle University and National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Heather Kerr
- Department of Chemistry, Edinburgh University, Edinburgh, UK; and
| | - Andrew P Herbert
- Department of Chemistry, Edinburgh University, Edinburgh, UK; and
| | - Paul N Barlow
- Department of Chemistry, Edinburgh University, Edinburgh, UK; and
| | | | - Kevin J Marchbank
- Institute of Cellular Medicine, Newcastle University and National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK;
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Sepuru KM, Iwahara J, Rajarathnam K. Direct detection of lysine side chain NH 3+ in protein-heparin complexes using NMR spectroscopy. Analyst 2018; 143:635-638. [PMID: 29292440 DOI: 10.1039/c7an01406f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two NMR observables, the NζH3+ peak in the HISQC spectrum and Nζ chemical shift difference between the free and heparin-bound forms, can identify binding-interface lysines in protein-heparin complexes. Unlike backbone chemical shifts, these direct probes are stringent and are less prone to either false positives or false negatives.
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Affiliation(s)
- Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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11
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Yang J, Chi L. Characterization of structural motifs for interactions between glycosaminoglycans and proteins. Carbohydr Res 2017; 452:54-63. [PMID: 29065343 DOI: 10.1016/j.carres.2017.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 11/24/2022]
Abstract
Glycosaminoglycans (GAGs) are a family of linear and anionic polysaccharides that play essential roles in many biological and physiological processes. Interactions between GAGs and proteins regulate function in many proteins and are related to many human diseases and disorders. The structural motifs and mechanisms for interactions between GAGs and proteins are not fully understood. Specific bindings, including minor but unique sequences sporadically distributed along the GAG chains or variably sulfated domains interspersed by undersulfated regions, may be specifically recognized by defined domains of a variety of proteins. Understanding the molecular basis of these interactions will provide a template for developing novel glycotherapeutic agents. The present article reviews recent methodologies and progress on the characterization of structural motifs in both GAGs and proteins involved in GAG-protein interactions. The analytical approaches are categorized into three groups: affinity-based methods; molecular docking, nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography; and mass spectrometry (MS) techniques. The advantages and limitations of each category of methods are discussed and are based on examples of using these techniques to investigate binding between GAGs and proteins.
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Affiliation(s)
- Jiyuan Yang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Jinan 250100, China.
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12
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Takechi-Haraya Y, Aki K, Tohyama Y, Harano Y, Kawakami T, Saito H, Okamura E. Glycosaminoglycan Binding and Non-Endocytic Membrane Translocation of Cell-Permeable Octaarginine Monitored by Real-Time In-Cell NMR Spectroscopy. Pharmaceuticals (Basel) 2017; 10:ph10020042. [PMID: 28420127 PMCID: PMC5490399 DOI: 10.3390/ph10020042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/13/2022] Open
Abstract
Glycosaminoglycans (GAGs), which are covalently-linked membrane proteins at the cell surface have recently been suggested to involve in not only endocytic cellular uptake but also non-endocytic direct cell membrane translocation of arginine-rich cell-penetrating peptides (CPPs). However, in-situ comprehensive observation and the quantitative analysis of the direct membrane translocation processes are challenging, and the mechanism therefore remains still unresolved. In this work, real-time in-cell NMR spectroscopy was applied to investigate the direct membrane translocation of octaarginine (R8) into living cells. By introducing 4-trifluoromethyl-l-phenylalanine to the N terminus of R8, the non-endocytic membrane translocation of 19F-labeled R8 (19F-R8) into a human myeloid leukemia cell line was observed at 4 °C with a time resolution in the order of minutes. 19F NMR successfully detected real-time R8 translocation: the binding to anionic GAGs at the cell surface, followed by the penetration into the cell membrane, and the entry into cytosol across the membrane. The NMR concentration analysis enabled quantification of how much of R8 was staying in the respective translocation processes with time in situ. Taken together, our in-cell NMR results provide the physicochemical rationale for spontaneous penetration of CPPs in cell membranes.
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Affiliation(s)
- Yuki Takechi-Haraya
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Kenzo Aki
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yumi Tohyama
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Yuichi Harano
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroyuki Saito
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto 607-8414, Japan.
| | - Emiko Okamura
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, 7-2-1 Kamiohno, Himeji 670-8524, Japan.
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Pomin VH, Mulloy B. Current structural biology of the heparin interactome. Curr Opin Struct Biol 2015; 34:17-25. [PMID: 26038285 DOI: 10.1016/j.sbi.2015.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/03/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
Abstract
Heparin is the best known therapeutically active carbohydrate. It can bind and regulate multiple functional proteins such as coagulation cofactors, chemokines, and growth factors. This versatility has led to the recently developed concept of the heparin interactome--a group of proteins that, as the name implies, interact with heparin. The heparin interactome is structurally and functionally diverse. Though natural ligands of this class of proteins may be any of the glycosaminoglycans however, their structural biology is generally studied using heparin as a model compound. NMR spectroscopy contributes significantly to structural investigations of the resultant complexes in solution. This review aims therefore at discussing the current status in structural biology of the molecular complexes formed between heparin and its protein partners through the current concept of the heparin interactome.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil.
| | - Barbara Mulloy
- Glycosciences Laboratory, Imperial College, Department of Medicine, Burlington Danes Building, Du Cane Road, London W12 0NN, UK.
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14
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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15
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NMR characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1851-9. [DOI: 10.1016/j.bbapap.2014.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 11/19/2022]
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16
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Esadze A, Zandarashvili L, Iwahara J. Effective strategy to assign ¹H- ¹⁵N heteronuclear correlation NMR signals from lysine side-chain NH3₃⁺ groups of proteins at low temperature. JOURNAL OF BIOMOLECULAR NMR 2014; 60:23-7. [PMID: 25129623 PMCID: PMC4160661 DOI: 10.1007/s10858-014-9854-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/06/2014] [Indexed: 05/15/2023]
Abstract
Recent studies have shown that lysine side-chain NH3(+) groups are excellent probes for NMR investigations of dynamics involving hydrogen bonds and ion pairs relevant to protein function. However, due to rapid hydrogen exchange, observation of (1)H-(15)N NMR cross peaks from lysine NH3(+) groups often requires use of a relatively low temperature, which renders difficulty in resonance assignment. Here we present an effective strategy to assign (1)H and (15)N resonances of NH3(+) groups at low temperatures. This strategy involves two new (1)H/(13)C/(15)N triple-resonance experiments for lysine side chains. Application to a protein-DNA complex is demonstrated.
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17
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Pomin VH. Biological findings from the recent NMR-based studies of glycosaminoglycan-protein interactions. Glycobiology 2014; 24:991-1003. [DOI: 10.1093/glycob/cwu065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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18
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De Paula VS, Pomin VH, Valente AP. Unique properties of human β-defensin 6 (hBD6) and glycosaminoglycan complex: sandwich-like dimerization and competition with the chemokine receptor 2 (CCR2) binding site. J Biol Chem 2014; 289:22969-22979. [PMID: 24970887 DOI: 10.1074/jbc.m114.572529] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Defensins are components of the innate immune system that promote the directional migration and activation of dendritic cells, thereby modulating the adaptive immune response. Because matrix glycosaminoglycan (GAG) is known to be important for these functions, we characterized the structural features of human β-defensin 6 (hBD6) and GAG interaction using a combination of structural and in silico analyses. Our results showed that GAG model compounds, a pentasaccharide (fondaparinux, FX) and an octasaccharide heparin derivative (dp8) bind to the α-helix and in the loops between the β2 and β3 strands, inducing the formation of a ternary complex with a 2:1 hBD6:FX stoichiometry. Competition experiments indicated an overlap of GAG and chemokine receptor CCR2 binding sites. An NMR-derived model of the ternary complex revealed that FX interacts with hBD6 along the dimerization interface, primarily contacting the α-helices and β2-β3 loops from each monomer. We further demonstrated that high-pressure NMR spectroscopy could capture an intermediate stage of hBD6-FX interaction, exhibiting features of a cooperative binding mechanism. Collectively, these data suggest a "sandwich-like" model in which two hBD6 molecules bind a single FX chain and provide novel structural insights into how defensin orchestrates leukocyte recruitment through GAG binding and G protein-coupled receptor activation. Despite the similarity to chemokines and hBD2, our data indicate different properties for the hBD6-GAG complex. This work adds significant information to the currently limited data available for the molecular structures and dynamics of defensin carbohydrate binding.
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Affiliation(s)
- Viviane S De Paula
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas and Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil.
| | - Vitor H Pomin
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas and Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil.
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Yuwen T, Skrynnikov NR. Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:155-169. [PMID: 24120537 DOI: 10.1016/j.jmr.2013.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
(15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We anticipate that the new experiment will be a valuable addition to the NMR toolbox for studies of IDPs.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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20
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Yuwen T, Skrynnikov NR. CP-HISQC: a better version of HSQC experiment for intrinsically disordered proteins under physiological conditions. JOURNAL OF BIOMOLECULAR NMR 2014; 58:175-92. [PMID: 24496557 DOI: 10.1007/s10858-014-9815-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/24/2014] [Indexed: 05/25/2023]
Abstract
(1)H-(15)N HSQC spectroscopy is a workhorse of protein NMR. However, under physiological conditions the quality of HSQC spectra tends to deteriorate due to fast solvent exchange. For globular proteins only a limited number of surface residues are affected, but in the case of intrinsically disordered proteins (IDPs) HSQC spectra are thoroughly degraded, suffering from both peak broadening and loss of intensity. To alleviate this problem, we make use of the following two concepts. (1) Proton-decoupled HSQC. Regular HSQC and its many variants record the evolution of multi-spin modes, 2NxHz or 2NxHx, in indirect dimension. Under the effect of fast solvent exchange these modes undergo rapid decay, which results in severe line-broadening. In contrast, proton-decoupled HSQC relies on Nx coherence which is essentially insensitive to the effects of solvent exchange. Moreover, for measurements involving IDPs at or near physiological temperature, Nx mode offers excellent relaxation properties, leading to very sharp resonances. (2) Cross-polarization (1)H-to-(15)N transfer. If CP element is designed such as to lock both (1)H(N) and water magnetization, the following transfer is effected: [Formula: see text] Thus water magnetization is successfully exploited to boost the amount of signal. In addition, CP element suffers less loss from solvent exchange, conformational exchange, and dipolar relaxation compared to the more popular INEPT element. Combining these two concepts, we have implemented the experiment termed CP-HISQC (cross-polarization assisted heteronuclear in-phase single-quantum correlation). The pulse sequence has been designed such as to preserve water magnetization and therefore can be executed with reasonably short recycling delays. In the presence of fast solvent exchange, kex ~ 100 s(-1), CP-HISQC offers much better spectral resolution than conventional HSQC-type experiments. At the same time it offers up to twofold gain in sensitivity compared to plain proton-decoupled HSQC. The new sequence has been tested on the sample of drkN SH3 domain at pH 7.5, 30 °C. High-quality spectrum has been recorded in less than 1 h, containing resonances from both folded and unfolded species. High-quality spectra have also been obtained for arginine side-chain H(ε)N(ε) groups in the sample of short peptide Sos. For Arg side chains, we have additionally implemented (HE)NE(CD)HD experiment. Using (13)C-labeled sample of Sos, we have demonstrated that proton-to-nitrogen CP transfer remains highly efficient in the presence of solvent exchange as fast as kex = 620 s(-1). In contrast, INEPT transfer completely fails in this regime.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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21
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Wang X, Liu Y, Wang H. A structure-differential binding method for elucidating the interactions between flavonoids and cytochrome-c by ESI-MS and molecular docking. Talanta 2013; 116:368-75. [DOI: 10.1016/j.talanta.2013.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/06/2013] [Accepted: 05/28/2013] [Indexed: 01/26/2023]
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22
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Jia L, Xu L, Wang Z, Xu J, Ji J. Label-free Fluorescent Sensor for Probing Heparin-Protein Interaction Based on Supramolecular Assemblies. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300086] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Lea SM, Johnson S. Putting the structure into complement. Immunobiology 2013; 217:1117-21. [PMID: 22964238 DOI: 10.1016/j.imbio.2012.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/13/2012] [Accepted: 07/15/2012] [Indexed: 11/25/2022]
Abstract
In a field where structure has finally begun to have a real impact, a series of new structures over the last two years have further extended our understanding of some of the critical regulatory events of the complement system. Notably, information has begun to flow from larger assemblies of components which allow insight into the often transient assemblies critical to complement regulation at the cell surface. This review will summarise the key structures determined since the last International Complement Workshop and the insights these have given us, before highlighting some questions that still require molecular frameworks to drive understanding.
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Affiliation(s)
- Susan M Lea
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
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24
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Chemokine oligomerization in cell signaling and migration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:531-78. [PMID: 23663982 DOI: 10.1016/b978-0-12-386931-9.00020-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemokines are small proteins best known for their role in controlling the migration of diverse cells, particularly leukocytes. Upon binding to their G-protein-coupled receptors on the leukocytes, chemokines stimulate the signaling events that cause cytoskeletal rearrangements involved in cell movement, and migration of the cells along chemokine gradients. Depending on the cell type, chemokines also induce many other types of cellular responses including those related to defense mechanisms, cell proliferation, survival, and development. Historically, most research efforts have focused on the interaction of chemokines with their receptors, where monomeric forms of the ligands are the functionally relevant state. More recently, however, the importance of chemokine interactions with cell surface glycosaminoglycans has come to light, and in most cases appears to involve oligomeric chemokine structures. This review summarizes existing knowledge relating to the structure and function of chemokine oligomers, and emerging methodology for determining structures of complex chemokine assemblies in the future.
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25
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Remko M, Duijnen PTV, Broer R. Structure and stability of complexes of charged structural units of heparin with arginine and lysine. RSC Adv 2013. [DOI: 10.1039/c2ra22062h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Wang X. Solution structure of decorin-binding protein A from Borrelia burgdorferi. Biochemistry 2012; 51:8353-62. [PMID: 22985470 DOI: 10.1021/bi3007093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Decorin-binding protein A (DBPA) is an important lipoprotein from the bacterium Borrelia burgdorferi, the causative agent of Lyme disease. The absence of DBPA drastically reduces the pathogenic potential of the bacterium, and biochemical evidence indicates DBPA's interactions with the glycosaminoglycan (GAG) portion of decorin are crucial to its function. We have determined the solution structure of DBPA and studied DBPA's interactions with various forms of GAGs. DBPA is determined to be a helical bundle protein consisting of five helices held together by a strong hydrophobic core. The structure also possesses a basic patch formed by portions of two helices and two flexible linkers. Low-molecular mass heparin-induced chemical shift perturbations for residues in the region as well as increases in signal intensities of select residues in their presence confirm residues in the pocket are perturbed by heparin binding. Dermatan sulfate fragments, the dominant GAG type found on decorin, were shown to have lower affinity than heparin but are still capable of binding DBPA.
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Affiliation(s)
- Xu Wang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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27
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Lebrun P, Raze D, Fritzinger B, Wieruszeski JM, Biet F, Dose A, Carpentier M, Schwarzer D, Allain F, Lippens G, Locht C. Differential contribution of the repeats to heparin binding of HBHA, a major adhesin of Mycobacterium tuberculosis. PLoS One 2012; 7:e32421. [PMID: 22403657 PMCID: PMC3293801 DOI: 10.1371/journal.pone.0032421] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 01/26/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Tuberculosis remains one of the most important causes of global mortality and morbidity, and the molecular mechanisms of the pathogenesis are still incompletely understood. Only few virulence factors of the causative agent Mycobacterium tuberculosis are known. One of them is the heparin-binding haemagglutinin (HBHA), an important adhesin for epithelial cells and an extrapulmonary dissemination factor. HBHA mediates mycobacterial adherence to epithelial cells via the interactions of its C-terminal, lysine rich repeat domain with sulfated glycoconjugates on the surface of epithelial cells. METHODOLOGY/PRINCIPAL FINDINGS Using defined heparin sulfate (HS) analogs, we determined the minimal heparin fragment length for HBHA binding and structural adaptations of the HBHA heparin-binding domain (HBD) upon binding to heparin. The NMR studies show significant shifts of all residues in the HBD upon interaction with heparin, with stronger shifts in the last repeats compared to the upstream repeats, and indicated that the HS fragments with 14 sugar units cover the entire C-terminal lysine-rich domain of HBHA. The differential implication of the repeats is determined by the relative position of prolines and lysines within each repeat, and may contribute to binding specificity. GAG binding induces a non-homogeneous structural rearrangement in the HBD, with stabilization of a nascent α-helix only in the last penta-repeats. CONCLUSION/SIGNIFICANCE Mycobacterial HBHA undergoes structural adaptation upon interaction with GAGs, which is likely involved in binding specificities of the adhesin, and mycobacterial pathogens may use HBD polymorphisms for host or organ specificity. Further studies will aim at decoding the complementarity between HBD repeats and HS sequence.
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Affiliation(s)
- Pierre Lebrun
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Lille, France
| | - Dominique Raze
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Lille, France
| | - Bernd Fritzinger
- Univ Lille Nord de France, Lille, France
- CNRS UMR8576 Structural and Functional Glycobiology, Villeneuve d'Ascq, France
| | - Jean-Michel Wieruszeski
- Univ Lille Nord de France, Lille, France
- CNRS UMR8576 Structural and Functional Glycobiology, Villeneuve d'Ascq, France
| | - Franck Biet
- UR1282, Infectiologie Animale, Sante' Publique (IASP-311), INRA, Nouzilly, France
| | - Alexander Dose
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Mathieu Carpentier
- Univ Lille Nord de France, Lille, France
- CNRS UMR8576 Structural and Functional Glycobiology, Villeneuve d'Ascq, France
| | - Dirk Schwarzer
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Fabrice Allain
- Univ Lille Nord de France, Lille, France
- CNRS UMR8576 Structural and Functional Glycobiology, Villeneuve d'Ascq, France
| | - Guy Lippens
- Univ Lille Nord de France, Lille, France
- CNRS UMR8576 Structural and Functional Glycobiology, Villeneuve d'Ascq, France
| | - Camille Locht
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Lille, France
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Pottiez G, Ciborowski P. Elucidating protein inter- and intramolecular interacting domains using chemical cross-linking and matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry. Anal Biochem 2012; 421:712-8. [PMID: 22226790 PMCID: PMC3287059 DOI: 10.1016/j.ab.2011.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/17/2011] [Accepted: 12/05/2011] [Indexed: 01/01/2023]
Abstract
Among many methods used to investigate protein/protein interactions, chemical cross-linking combined with mass spectrometry remains a vital experimental approach. Mapping peptides modified by cross-linker provides clues about proteins' interacting domains. One complication is that such modification may result from intra- but not intermolecular interactions. Therefore, for overall data interpretation, a combination of results from various platforms is necessary. It is postulated that the secretory isoform of gelsolin regulates several biological processes through interactions with proteins such as actin, fibronectin, vitamin D-binding protein, and unidentified receptors on the surface of eukaryotes; it also has been shown to self-assemble eventually leading to the formation of homo-multimers. As such, it is an excellent model for this study. We used four cross-linkers with arm length ranging from 7.7 to 21.7Å and MALDI-TOF/TOF mass spectrometry as the analytical platform. Results of this study show that MALDI-based mass spectrometry generates high quality data to show lysine residues modified by cross-linkers and combined with existing data based on crystallography (Protein Data Bank, PDB) can be used to discriminate between inter- and intramolecular linking.
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Affiliation(s)
- Gwënaël Pottiez
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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29
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Chen WT, Chiang CK, Lee CH, Chang HT. Using surface-assisted laser desorption/ionization mass spectrometry to detect proteins and protein-protein complexes. Anal Chem 2012; 84:1924-30. [PMID: 22264081 DOI: 10.1021/ac202883q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study, we combined surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) with HgTe nanostructures as matrix for the detection of several proteins (α1-antitrypsin, trypsin, IgG, protein G) and their complexes. We investigated the effects of several parameters (the concentration and nature of surfactants and metal ions, the pH, and concentration of the analytes in the sample matrixes) on the sensitivity of the detection of these proteins and their complexes. The presence of stabilizing Brij 76 surfactant and Zn(II) ions allowed the detection of weak protein complexes, such as α1-antitrypsin-trypsin and IgG-protein G complexes, at the picomole level. We observed multiply charged states at m/z 72,160 ([α1-antitrypsin + trypsin + H](+)) and 86,585 ([IgG + protein G + 2H](2+)) for the α1-antitrypsin-trypsin and IgG-protein G complexes, respectively. To the best of our knowledge, detection of weak protein complexes and determination of their stoichiometry have not been demonstrated previously when a combination of SALDI-MS and nanostructures were used. This simple and reproducible SALDI-MS approach using HgTe nanostructures holds great potential for the detection of other proteins and their complexes.
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Affiliation(s)
- Wen-Tsen Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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30
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Chen FF, Lin WH, Lin SC, Kuo JH, Chu HY, Huang WC, Chuang YJ, Lee SC, Sue SC. Significance of heparin binding to basic residues in homologous to the amino terminus of hepatoma-derived growth factor and related proteins. Glycobiology 2012; 22:649-61. [DOI: 10.1093/glycob/cwr191] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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31
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Helix formation and capping energetics of arginine analogs with varying side chain length. Amino Acids 2011; 43:195-206. [PMID: 21922267 DOI: 10.1007/s00726-011-1064-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 08/20/2011] [Indexed: 10/17/2022]
Abstract
Arginine (Arg) has been used for recognizing negatively charged biological molecules, cell penetration, and oligosaccharide mass signal enhancement. The versatility of Arg has inspired the need to develop Arg analogs and to research the structural effects of incorporating Arg analogs. Accordingly, we investigated the effect of Arg side chain length on helix formation by studying 12 Ala-based peptides containing the Arg analogs (S)-2-amino-6-guanidino-hexanoic acid (Agh), (S)-2-amino-4-guanidinobutyric acid (Agb), and (S)-2-amino-3-guanidinopropionic acid (Agp). Solid phase guanidinylation with orthogonal protection strategies was necessary to synthesize Agb- and Agp-containing peptides using Fmoc-based chemistry. The fraction helix for the peptides was determined by circular dichroism spectroscopy, and used to derive the statistical mechanical parameters and energetics for N-capping, C-capping, and helix propagation (propensity). All four Arg analogs were unfavorable for N-capping. The C-cap parameter followed the trend Agp<Agb<Arg<Agh, showing more favorable C-cap energetics with increasing side chain length. In contrast, helix propensity followed the trend Agp<Agb<Arg>Agh, highlighting the uniqueness of the Arg side chain length in helix formation. Molecular mechanics calculations and a survey on protein structures were consistent with the experimental results. Furthermore, calculations and survey both showed that the g- conformation for the χ1 dihedral was present for the first two residues at the N-terminus of helices, but not favored in the center or C-terminus of helices due to sterics. These results should serve as the foundation for developing Arg-related bioactive compounds and technologies.
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32
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Esadze A, Li DW, Wang T, Brüschweiler R, Iwahara J. Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy. J Am Chem Soc 2011; 133:909-19. [PMID: 21186799 DOI: 10.1021/ja107847d] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics of lysine NH3(+) groups by NMR spectroscopy and computation. By using 1H−15N heteronuclear correlation experiments optimized for 15NH3(+) moieties, we have analyzed the dynamic behavior of individual lysine NH3(+) groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH3 groups and used it to analyze 15N relaxation data for the NH3(+) groups. For six lysine NH3(+) groups out of seven in ubiquitin, we have determined model-free order parameters, correlation times for bond rotation, and reorientation of the symmetry axis occurring on a pico- to nanosecond time scale. From CPMG relaxation dispersion experiment for lysine NH3(+) groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH3(+) groups of Lys48, which plays a key role as the linkage site in ubiquitination for proteasomal degradation, was found to be highly mobile with the lowest order parameter among the six NH3(+) groups analyzed by NMR. We compared the experimental order parameters for the lysine NH3(+) groups with those from a 1 μs molecular dynamics simulation in explicit solvent and found good agreement between the two. Furthermore, both the computer simulation and the experimental correlation times for the bond rotations of NH3(+) groups suggest that their hydrogen bonding is highly dynamic with a subnanosecond lifetime. This study demonstrates the utility of combining NMR experiment and simulation for an in-depth characterization of the dynamics of these functionally most important side-chains of ubiquitin.
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Affiliation(s)
- Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
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Scambi C, La Verde V, De Franceschi L, Barausse G, Poli F, Benedetti F, Sorio M, Deriu F, Roncada P, Bortolami O, Turrini F, Caramaschi P, Stranieri C, Bambara LM, Biasi D. Comparative proteomic analysis of serum from patients with systemic sclerosis and sclerodermatous GVHD. Evidence of defective function of factor H. PLoS One 2010; 5:e12162. [PMID: 20730046 PMCID: PMC2921355 DOI: 10.1371/journal.pone.0012162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 06/13/2010] [Indexed: 01/07/2023] Open
Abstract
Background Systemic sclerosis (SSc) is an autoimmune disease characterized by immunological and vascular abnormalities. Until now, the cause of SSc remains unclear. Sclerodermatous graft-versus-host disease (ScGVHD) is one of the most severe complications following bone marrow transplantation (BMT) for haematological disorders. Since the first cases, the similarity of ScGVHD to SSc has been reported. However, both diseases could have different etiopathogeneses. The objective of this study was to identify new serum biomarkers involved in SSc and ScGVHD. Methodology Serum was obtained from patients with SSc and ScGVHD, patients without ScGVHD who received BMT for haematological disorders and healthy controls. Bi-dimensional electrophoresis (2D) was carried out to generate maps of serum proteins from patients and controls. The 2D maps underwent image analysis and differently expressed proteins were identified. Immuno-blot analysis and ELISA assay were used to validate the proteomic data. Hemolytic assay with sheep erythrocytes was performed to evaluate the capacity of Factor H (FH) to control complement activation on the cellular surface. FH binding to endothelial cells (ECs) was also analysed in order to assess possible dysfunctions of this protein. Principal Findings Fourteen differentially expressed proteins were identified. We detected pneumococcal antibody cross-reacting with double stranded DNA in serum of all bone marrow transplanted patients with ScGVHD. We documented higher levels of FH in serum of SSc and ScGVHD patients compared healthy controls and increased sheep erythrocytes lysis after incubation with serum of diffuse SSc patients. In addition, we observed that FH binding to ECs was reduced when we used serum from these patients. Conclusions The comparative proteomic analysis of serum from SSc and ScGVHD patients highlighted proteins involved in either promoting or maintaining an inflammatory state. We also found a defective function of Factor H, possibly associated with ECs damage.
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Affiliation(s)
- Cinzia Scambi
- Section of Rheumatology, Department of Clinical and Experimental Medicine, University of Verona, Verona, Italy.
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