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Saad MH, El-Fakharany EM, Salem MS, Sidkey NM. In vitro assessment of dual (antiviral and antitumor) activity of a novel lectin produced by the newly cyanobacterium isolate, Oscillatoria acuminate MHM-632 MK014210.1. J Biomol Struct Dyn 2022; 40:3560-3580. [PMID: 33200676 DOI: 10.1080/07391102.2020.1848632] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/04/2020] [Indexed: 02/02/2023]
Abstract
A novel lectin was purified from newly cyanobacterium isolate, Oscillatoria acuminate MHM-632 MK014210.1 using affinity chromatography with a molecular weight of 120 kDa under native-PAGE and 30 kDa on reducing-PAGE, represented tetramer nature of this lectin. Oscillatorial lectin showed stability at 60 °C for 30 min, pH-dependent, with the highest activities over the pH range of 6-8, and required zinc ions to express its full activity. Oscillatorial lectin is a glycan-binding protein with a neutral carbohydrate content of 7.0% as evaluated by the phenol-sulfuric acid method. Polyols and α- glycosides polymer of mannose sugar or sugars alcohol were completely inhibited oscillatorial lectin with MIC of 0.195 mM, while β-glycosides sugars did not show any inhibition effect. The oscillatorial lectin has anti-proliferative activity against Huh-7 and MCF-7 cancer cells and inhibited their proliferation with EC50 values of 106.75 µg/ml and 254.14 µg/ml, respectively. Besides the anticancer effect, oscillatorial lectin also has potent antiviral activity against HSV-1 in a dose-dependent manner via virions neutralization and inhibition of viral replication with IC50 values of 90.95 ng/ml and 131.3 ng/ml, respectively. The unique carbohydrate affinity of oscillatorial lectin provides insight into its use as a promising candidate in many biotechnological applications, like fighting viral infection and combating cancer disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mabroka H Saad
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
- Botany & Microbiology Department, Faculty of Science, Al Azhar University (Girls Branch), Nasr City, Egypt
| | - Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Marwa S Salem
- Botany & Microbiology Department, Faculty of Science, Al Azhar University (Girls Branch), Nasr City, Egypt
| | - Nagwa M Sidkey
- Botany & Microbiology Department, Faculty of Science, Al Azhar University (Girls Branch), Nasr City, Egypt
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Kazan IC, Sharma P, Rahman MI, Bobkov A, Fromme R, Ghirlanda G, Ozkan SB. Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations. eLife 2022; 11:67474. [PMID: 36472898 PMCID: PMC9725752 DOI: 10.7554/elife.67474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
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Affiliation(s)
- I Can Kazan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States,School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Prerna Sharma
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | | | - Andrey Bobkov
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - S Banu Ozkan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
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Sangtani R, Ghosh A, Jha HC, Parmar HS, Bala K. Potential of algal metabolites for the development of broad-spectrum antiviral therapeutics: Possible implications in COVID-19 therapy. Phytother Res 2021; 35:2296-2316. [PMID: 33210447 PMCID: PMC7753317 DOI: 10.1002/ptr.6948] [Citation(s) in RCA: 9] [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: 07/03/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/25/2023]
Abstract
Covid-19 pandemic severely affected human health worldwide. Till October 19, 2020, total confirmed patients of COVID-19 are 39,944,882, whereas 1,111,998 people died across the globe. Till to date, we do not have any specific medicine and/or vaccine to treat COVID-19; however, research is still going on at war footing. So far vaccine development is concerned, here it is noteworthy that till now three major variants (named A, B, and C) of severe acute respiratory syndrome-coronavirus2 (SARS-CoV-2) have been recognized. Increased mutational rate and formation of new viral variants may increase the attrition rate of vaccines and/or candidate chemotherapies. Herbal remedies are chemical cocktails, thus open another avenue for effective antiviral therapeutics development. In fact, India is a large country, which is densely populated, but the overall severity of COVID-19 per million populations is lesser than any other country of the world. One of the major reasons for the aforesaid difference is the use of herbal remedies by the Government of India as a preventive measure for COVID-19. Therefore, the present review focuses on the epidemiology and molecular pathogenesis of COVID-19 and explores algal metabolites for their antiviral properties.
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Affiliation(s)
- Rimjhim Sangtani
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | - Atreyee Ghosh
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | - Hem C. Jha
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | | | - Kiran Bala
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
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Lin B, Qing X, Liao J, Zhuo K. Role of Protein Glycosylation in Host-Pathogen Interaction. Cells 2020; 9:E1022. [PMID: 32326128 PMCID: PMC7226260 DOI: 10.3390/cells9041022] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
Host-pathogen interactions are fundamental to our understanding of infectious diseases. Protein glycosylation is one kind of common post-translational modification, forming glycoproteins and modulating numerous important biological processes. It also occurs in host-pathogen interaction, affecting host resistance or pathogen virulence often because glycans regulate protein conformation, activity, and stability, etc. This review summarizes various roles of different glycoproteins during the interaction, which include: host glycoproteins prevent pathogens as barriers; pathogen glycoproteins promote pathogens to attack host proteins as weapons; pathogens glycosylate proteins of the host to enhance virulence; and hosts sense pathogen glycoproteins to induce resistance. In addition, this review also intends to summarize the roles of lectin (a class of protein entangled with glycoprotein) in host-pathogen interactions, including bacterial adhesins, viral lectins or host lectins. Although these studies show the importance of protein glycosylation in host-pathogen interaction, much remains to be discovered about the interaction mechanism.
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Affiliation(s)
- Borong Lin
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, China; (B.L.); (J.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Xue Qing
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jinling Liao
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, China; (B.L.); (J.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
- Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
| | - Kan Zhuo
- Laboratory of Plant Nematology, South China Agricultural University, Guangzhou 510642, China; (B.L.); (J.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
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Jan M, Upadhyay C, Alcami Pertejo J, Hioe CE, Arora SK. Heterogeneity in glycan composition on the surface of HIV-1 envelope determines virus sensitivity to lectins. PLoS One 2018; 13:e0194498. [PMID: 29579062 PMCID: PMC5868795 DOI: 10.1371/journal.pone.0194498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/05/2018] [Indexed: 01/08/2023] Open
Abstract
Lectins that target N-glycans on the surface of HIV-1 envelope (Env) glycoprotein have the potential for use as antiviral agents. Although progress has been made in deciphering the molecular details of lectin and Env glycan interaction, further studies are needed to better understand Env glycan heterogeneity among HIV-1 isolates and its influence on virus-neutralization sensitivity to lectins. This study evaluated a panel of lectins with fine specificity for distinct oligosaccharides and assessed their ability to inhibit infection of HIV-1 viruses known to have differing sensitivity to anti-HIV Env antibodies. The results showed that HIV-1 isolates have different sensitivity to lectins specific for α1-3Man, α1-6Man, and α1-2Man binding lectins. Considering that lectins exclusively recognize the oligosaccharide components of virus Env, these data suggest that glycan heterogeneity among HIV-1 isolates may explain this differential sensitivity. To evaluate this further, chronic and acute viruses were produced in the presence of different glycosidase inhibitors to express more homogenous glycans. Viruses enriched for α1-2Man terminating Man5-9GlcNAc2 glycans became similarly sensitive to α1-2Man-binding lectins. The α1-3Man- and α1-6Man-binding lectins also were more potent against viruses expressing predominantly Man5GlcNAc2 and hybrid type glycans with terminal α1-3Man and α1-6Man. Furthermore, lectin-mediated inhibition was competitively alleviated by mannan and this effect was augmented by enrichment of mannose-type glycans on the virus. In addition, while Env of viruses enriched with mannose-type glycans were sensitive to Endo-H deglycosylation, Env of untreated viruses were partially resistant, indicating that HIV-1 Env glycans are heterogeneously comprised of complex, hybrid, and mannose types. Overall, our data demonstrate that HIV-1 isolates display differential sensitivity to lectins, in part due to the microheterogeneity of N-linked glycans expressed on the surface of the virus Env glycoprotein.
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Affiliation(s)
- Muzafar Jan
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- James J. Peters VA Medical Center, Bronx, New York, United States of America
| | - Chitra Upadhyay
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - José Alcami Pertejo
- Imunopatologia Del SIDA, Centro Nacional De Microbiologia, Instituo De Salud Carlos III, Madrid, Spain
| | - Catarina E. Hioe
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- James J. Peters VA Medical Center, Bronx, New York, United States of America
| | - Sunil K. Arora
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
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Abstract
Advances in protein engineering tools, both computational and experimental, has afforded many new protein structures and functions. Here, we present a snapshot of repeat-protein engineering efforts towards new, versatile, alternative binding scaffolds for use in analytical sensors and as imaging agents. Analytical assays, sensors and imaging agents based on the direct binding of analyte are increasingly important for research and diagnostics in medicine, food safety, and national security.
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Woodrum BW, Maxwell J, Allen DM, Wilson J, Krumpe LRH, Bobkov AA, Hill RB, Kibler KV, O'Keefe BR, Ghirlanda G. A Designed "Nested" Dimer of Cyanovirin-N Increases Antiviral Activity. Viruses 2016; 8:v8060158. [PMID: 27275831 PMCID: PMC4926178 DOI: 10.3390/v8060158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 12/19/2022] Open
Abstract
Cyanovirin-N (CV-N) is an antiviral lectin with potent activity against enveloped viruses, including HIV. The mechanism of action involves high affinity binding to mannose-rich glycans that decorate the surface of enveloped viruses. In the case of HIV, antiviral activity of CV-N is postulated to require multivalent interactions with envelope protein gp120, achieved through a pseudo-repeat of sequence that adopts two near-identical glycan-binding sites, and possibly involves a 3D-domain-swapped dimeric form of CV-N. Here, we present a covalent dimer of CV-N that increases the number of active glycan-binding sites, and we characterize its ability to recognize four glycans in solution. A CV-N variant was designed in which two native repeats were separated by the “nested” covalent insertion of two additional repeats of CV-N, resulting in four possible glycan-binding sites. The resulting Nested CV-N folds into a wild-type-like structure as assessed by circular dichroism and NMR spectroscopy, and displays high thermal stability with a Tm of 59 °C, identical to WT. All four glycan-binding domains encompassed by the sequence are functional as demonstrated by isothermal titration calorimetry, which revealed two sets of binding events to dimannose with dissociation constants Kd of 25 μM and 900 μM, assigned to domains B and B’ and domains A and A’ respectively. Nested CV-N displays a slight increase in activity when compared to WT CV-N in both an anti-HIV cellular assay and a fusion assay. This construct conserves the original binding specifityies of domain A and B, thus indicating correct fold of the two CV-N repeats. Thus, rational design can be used to increase multivalency in antiviral lectins in a controlled manner.
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Affiliation(s)
- Brian W Woodrum
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Jason Maxwell
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Denysia M Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| | - Jennifer Wilson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Karen V Kibler
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Barry R O'Keefe
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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Cheung RCF, Wong JH, Pan W, Chan YS, Yin C, Dan X, Ng TB. Marine lectins and their medicinal applications. Appl Microbiol Biotechnol 2015; 99:3755-73. [PMID: 25794876 PMCID: PMC7080081 DOI: 10.1007/s00253-015-6518-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 12/16/2022]
Abstract
Marine organisms have been extensively explored for the last several decades as potential sources of novel biologically active compounds, and extensive research has been conducted on lectins. Lectins derived from marine organisms are structurally diverse and also differ from those identified from terrestrial organisms. Marine lectins appear to be particularly useful in some biological applications. They seem to induce negligible immunogenicity because they have a relatively small size, are more stable due to extensive disulfide bridge formation, and have high specificity for complex glyco-conjugates and carbohydrates instead of simple sugars. It is clear that many of them have not yet been extensively studied when compared with their terrestrial counterparts. Marine lectins can be used to design and develop new potentially useful therapeutic agents. This review encompasses recent research on the isolation and identification of marine lectins with potential value in medicinal applications.
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Affiliation(s)
- Randy Chi Fai Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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Akkouh O, Ng TB, Singh SS, Yin C, Dan X, Chan YS, Pan W, Cheung RCF. Lectins with anti-HIV activity: a review. Molecules 2015; 20:648-68. [PMID: 25569520 PMCID: PMC6272367 DOI: 10.3390/molecules20010648] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 11/29/2014] [Indexed: 11/18/2022] Open
Abstract
Lectins including flowering plant lectins, algal lectins, cyanobacterial lectins, actinomycete lectin, worm lectins, and the nonpeptidic lectin mimics pradimicins and benanomicins, exhibit anti-HIV activity. The anti-HIV plant lectins include Artocarpus heterophyllus (jacalin) lectin, concanavalin A, Galanthus nivalis (snowdrop) agglutinin-related lectins, Musa acuminata (banana) lectin, Myrianthus holstii lectin, Narcissus pseudonarcissus lectin, and Urtica diocia agglutinin. The anti-HIV algal lectins comprise Boodlea coacta lectin, Griffithsin, Oscillatoria agardhii agglutinin. The anti-HIV cyanobacterial lectins are cyanovirin-N, scytovirin, Microcystis viridis lectin, and microvirin. Actinohivin is an anti-HIV actinomycete lectin. The anti-HIV worm lectins include Chaetopterus variopedatus polychaete marine worm lectin, Serpula vermicularis sea worm lectin, and C-type lectin Mermaid from nematode (Laxus oneistus). The anti-HIV nonpeptidic lectin mimics comprise pradimicins and benanomicins. Their anti-HIV mechanisms are discussed.
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Affiliation(s)
- Ouafae Akkouh
- Department of Biology and Medical Laboratory Research, Faculty of Technology, University of Applied Sciences Leiden, Zernikdreef 11, 2333 CK Leiden, The Netherlands.
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Senjam Sunil Singh
- Department of Biochemistry, Manipur University, Canchipur, Imphal 795003, India.
| | - Cuiming Yin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xiuli Dan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Yau Sang Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Wenliang Pan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Randy Chi Fai Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Bolia A, Woodrum BW, Cereda A, Ruben MA, Wang X, Ozkan SB, Ghirlanda G. A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding. Biophys J 2014; 106:1142-51. [PMID: 24606938 DOI: 10.1016/j.bpj.2014.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 01/10/2023] Open
Abstract
Cyanovirin-N (CVN), a cyanobacterial lectin, exemplifies a class of antiviral agents that inhibit HIV by binding to the highly glycosylated envelope protein gp120. Here, we investigate the energetics of glycan recognition using a computationally inexpensive flexible docking approach, backbone perturbation docking (BP-Dock). We benchmarked our method using two mutants of CVN: P51G-m4-CVN, which binds dimannose with high affinity through domain B, and CVN((mutDB)), in which binding to domain B has been abolished through mutation of five polar residues to small nonpolar side chains. We investigated the energetic contribution of these polar residues along with the additional position 53 by docking dimannose to single-point CVN mutant models. Analysis of the docking simulations indicated that the E41A/G and T57A mutations led to a significant decrease in binding energy scores due to rearrangements of the hydrogen-bond network that reverberated throughout the binding cavity. N42A decreased the binding score to a level comparable to that of CVN((mutDB)) by affecting the integrity of the local protein structure. In contrast, N53S resulted in a high binding energy score, similar to P51G-m4-CVN. Experimental characterization of the five mutants by NMR spectroscopy confirmed the binding affinity pattern predicted by BP-Dock. Despite their mostly conserved fold and stability, E41A, E41G, and T57A displayed dissociation constants in the millimolar range. N53S showed a binding constant in the low micromolar range, similar to that observed for P51G-m4-CVN. No binding was observed for N42A. Our results show that BP-Dock is a useful tool for rapidly screening the relative binding affinity pattern of in silico-designed mutants compared with wild-type, supporting its use to design novel mutants with enhanced binding properties.
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Affiliation(s)
- Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Brian W Woodrum
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Angelo Cereda
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Melissa A Ruben
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - Xu Wang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona.
| | - Giovanna Ghirlanda
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona.
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Parker R, Mercedes-Camacho A, Grove TZ. Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment. Protein Sci 2014; 23:790-800. [PMID: 24659515 DOI: 10.1002/pro.2461] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 12/19/2022]
Abstract
Repeat proteins have recently emerged as especially well-suited alternative binding scaffolds due to their modular architecture and biophysical properties. Here we present the design of a scaffold based on the consensus sequence of the leucine rich repeat (LRR) domain of the NOD family of cytoplasmic innate immune system receptors. Consensus sequence design has emerged as a protein design tool to create de novo proteins that capture sequence-structure relationships and interactions present in nature. The multiple sequence alignment of 311 individual LRRs, which are the putative ligand-recognition domain in NOD proteins, resulted in a consensus sequence protein containing two internal and N- and C-capping repeats named CLRR2. CLRR2 protein is a stable, monomeric, and cysteine free scaffold that without any affinity maturation displays micromolar binding to muramyl dipeptide, a bacterial cell wall fragment. To our knowledge, this is the first report of direct interaction of a NOD LRR with a physiologically relevant ligand.
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Affiliation(s)
- Rachael Parker
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, 24060
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