1
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Mutational signatures in GATA3 transcription factor and its DNA binding domain that stimulate breast cancer and HDR syndrome. Sci Rep 2021; 11:22762. [PMID: 34815386 PMCID: PMC8611019 DOI: 10.1038/s41598-021-01832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Transcription factors (TFs) play important roles in many biochemical processes. Many human genetic disorders have been associated with mutations in the genes encoding these transcription factors, and so those mutations became targets for medications and drug design. In parallel, since many transcription factors act either as tumor suppressors or oncogenes, their mutations are mostly associated with cancer. In this perspective, we studied the GATA3 transcription factor when bound to DNA in a crystal structure and assessed the effect of different mutations encountered in patients with different diseases and phenotypes. We generated all missense mutants of GATA3 protein and DNA within the adjacent and the opposite GATA3:DNA complex models. We mutated every amino acid and studied the new binding of the complex after each mutation. Similarly, we did for every DNA base. We applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations. After analyzing our data, we identified amino acids and DNA bases keys for binding. Furthermore, we validated those findings against experimental genetic data. Our results are the first to propose in silico modeling for GATA:DNA bound complexes that could be used to score effects of missense mutations in other classes of transcription factors involved in common and genetic diseases.
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2
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Sequeiros-Borja CE, Surpeta B, Brezovsky J. Recent advances in user-friendly computational tools to engineer protein function. Brief Bioinform 2021; 22:bbaa150. [PMID: 32743637 PMCID: PMC8138880 DOI: 10.1093/bib/bbaa150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein-protein and protein-nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
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Affiliation(s)
- Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw
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3
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Narkhede YB, Gautam AK, Hsu RV, Rodriguez W, Zewde NT, Harrison RES, Arantes PR, Gaieb Z, Gorham RD, Kieslich C, Morikis D, Sahu A, Palermo G. Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition. Front Mol Biosci 2021; 8:618068. [PMID: 33829039 PMCID: PMC8020814 DOI: 10.3389/fmolb.2021.618068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
Poxviruses are dangerous pathogens, which can cause fatal infection in unvaccinated individuals. The causative agent of smallpox in humans, variola virus, is closely related to the bovine vaccinia virus, yet the molecular basis of their selectivity is currently incompletely understood. Here, we examine the role of the electrostatics in the selectivity of the smallpox protein SPICE and vaccinia protein VCP toward the human and bovine complement protein C3b, a key component of the complement immune response. Electrostatic calculations, in-silico alanine-scan and electrostatic hotspot analysis, as introduced by Kieslich and Morikis (PLoS Comput. Biol. 2012), are used to assess the electrostatic complementarity and to identify sites resistant to local perturbation where the electrostatic potential is likely to be evolutionary conserved. The calculations suggest that the bovine C3b is electrostatically prone to selectively bind its VCP ligand. On the other hand, the human isoform of C3b exhibits a lower electrostatic complementarity toward its SPICE ligand. Yet, the human C3b displays a highly preserved electrostatic core, which suggests that this isoform could be less selective in binding different ligands like SPICE and the human Factor H. This is supported by experimental cofactor activity assays revealing that the human C3b is prone to bind both SPICE and Factor H, which exhibit diverse electrostatic properties. Additional investigations considering mutants of SPICE and VCP that revert their selectivity reveal an “electrostatic switch” into the central modules of the ligands, supporting the critical role of the electrostatics in the selectivity. Taken together, these evidences provide insights into the selectivity mechanism of the complement regulator proteins encoded by the variola and vaccinia viruses to circumvent the complement immunity and exert their pathogenic action. These fundamental aspects are valuable for the development of novel vaccines and therapeutic strategies.
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Affiliation(s)
- Yogesh B Narkhede
- Department of Bioengineering, University of California, Riverside, CA
| | - Avneesh K Gautam
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, India
| | - Rohaine V Hsu
- Department of Bioengineering, University of California, Riverside, CA
| | - Wilson Rodriguez
- Department of Bioengineering, University of California, Riverside, CA
| | - Nehemiah T Zewde
- Department of Bioengineering, University of California, Riverside, CA
| | - Reed E S Harrison
- Department of Bioengineering, University of California, Riverside, CA
| | - Pablo R Arantes
- Department of Bioengineering, University of California, Riverside, CA
| | - Zied Gaieb
- Department of Bioengineering, University of California, Riverside, CA
| | - Ronald D Gorham
- Department of Bioengineering, University of California, Riverside, CA
| | - Chris Kieslich
- Department of Bioengineering, University of California, Riverside, CA.,Department of Chemical Engineering, Auburn University, Auburn, AL
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, CA
| | - Arvind Sahu
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, India
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, CA.,Department of Chemistry, University of California, Riverside, CA
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4
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Harrison RES, Zewde NT, Narkhede YB, Hsu RV, Morikis D, Vullev VI, Palermo G. Factor H-Inspired Design of Peptide Biomarkers of the Complement C3d Protein. ACS Med Chem Lett 2020; 11:1054-1059. [PMID: 32435425 DOI: 10.1021/acsmedchemlett.9b00663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/28/2020] [Indexed: 01/12/2023] Open
Abstract
C3d is a hallmark protein of the complement system, whose presence is critical to measure the progression of several immune diseases. Here, we propose to directly target C3d through small peptides mimicking the binding of its natural ligand, the complement regulator Factor H (FH). Through iterative computational analysis and binding affinity experiments, we establish a rationale for the structure-based design of FH-inspired peptides, leading to low-micromolar affinity for C3d and stable binding over microsecond-length simulations. Our FH-inspired peptides call now for further optimization toward high-affinity binding and suggest that small peptides are promising as novel C3d biomarkers and therapeutic tools.
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5
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AESOP: A Python Library for Investigating Electrostatics in Protein Interactions. Biophys J 2017; 112:1761-1766. [PMID: 28494947 DOI: 10.1016/j.bpj.2017.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/07/2017] [Accepted: 04/06/2017] [Indexed: 11/24/2022] Open
Abstract
Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association.
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6
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López-Perrote A, Harrison RES, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O. Ionic tethering contributes to the conformational stability and function of complement C3b. Mol Immunol 2017; 85:137-147. [PMID: 28254726 DOI: 10.1016/j.molimm.2016.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 11/28/2022]
Abstract
C3b, the central component of the alternative pathway (AP) of the complement system, coexists as a mixture of conformations in solution. These conformational changes can affect interactions with other proteins and complement regulators. Here we combine a computational model for electrostatic interactions within C3b with molecular imaging to study the conformation of C3b. The computational analysis shows that the TED domain in C3b is tethered ionically to the macroglobulin (MG) ring. Monovalent counterion concentration affects the magnitude of electrostatic forces anchoring the TED domain to the rest of the C3b molecule in a thermodynamic model. This is confirmed by observing NaCl concentration dependent conformational changes using single molecule electron microscopy (EM). We show that the displacement of the TED domain is compatible with C3b binding to Factor B (FB), suggesting that the regulation of the C3bBb convertase could be affected by conditions that promote movement in the TED domain. Our molecular model also predicts mutations that could alter the positioning of the TED domain, including the common R102G polymorphism, a risk variant for developing age-related macular degeneration. The common C3b isoform, C3bS, and the risk isoform, C3bF, show distinct energetic barriers to displacement in the TED that are related to a network of electrostatic interactions at the interface of the TED and MG-ring domains of C3b. These computational predictions agree with experimental evidence that shows differences in conformation observed in C3b isoforms purified from homozygous donors. Altogether, we reveal an ionic, reversible attachment of the TED domain to the MG ring that may influence complement regulation in some mutations and polymorphisms of C3b.
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Affiliation(s)
- Andrés López-Perrote
- Centro de Investigaciones Biológicas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Reed E S Harrison
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Marta Subías
- Centro de Investigaciones Biológicas, Spanish National Research Council (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Enfermedades Raras, Madrid, Spain
| | - Martín Alcorlo
- Centro de Investigaciones Biológicas, Spanish National Research Council (CSIC), Madrid, Spain
| | - Santiago Rodríguez de Córdoba
- Centro de Investigaciones Biológicas, Spanish National Research Council (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Enfermedades Raras, Madrid, Spain.
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Spanish National Research Council (CSIC), Madrid, Spain.
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7
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Zhang Y, Guo J, Li L, Liu X, Yao X, Liu H. The solvent at antigen-binding site regulated C3d–CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation. Biochim Biophys Acta Gen Subj 2016; 1860:2220-31. [DOI: 10.1016/j.bbagen.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
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8
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Abstract
![]()
Electrostatic effects
are ubiquitous in protein interactions and
are found to be pervasive in the complement system as well. The interaction
between complement fragment C3d and complement receptor 2 (CR2) has
evolved to become a link between innate and adaptive immunity. Electrostatic
interactions have been suggested to be the driving factor for the
association of the C3d:CR2 complex. In this study, we investigate
the effects of ionic strength and mutagenesis on the association of
C3d:CR2 through Brownian dynamics simulations. We demonstrate that
the formation of the C3d:CR2 complex is ionic strength-dependent,
suggesting the presence of long-range electrostatic steering that
accelerates the complex formation. Electrostatic steering occurs through
the interaction of an acidic surface patch in C3d and the positively
charged CR2 and is supported by the effects of mutations within the
acidic patch of C3d that slow or diminish association. Our data are
in agreement with previous experimental mutagenesis and binding studies
and computational studies. Although the C3d acidic patch may be locally
destabilizing because of unfavorable Coulombic interactions of like
charges, it contributes to the acceleration of association. Therefore,
acceleration of function through electrostatic steering takes precedence
to stability. The site of interaction between C3d and CR2 has been
the target for delivery of CR2-bound nanoparticle, antibody, and small
molecule biomarkers, as well as potential therapeutics. A detailed
knowledge of the physicochemical basis of C3d:CR2 association may
be necessary to accelerate biomarker and drug discovery efforts.
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Affiliation(s)
- Rohith R Mohan
- Department of Bioengineering, University of California , Riverside, California 92521, United States
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California , San Diego, California 92093, United States
| | - Dimitrios Morikis
- Department of Bioengineering, University of California , Riverside, California 92521, United States
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9
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Gorham RD, Nuñez V, Lin JH, Rooijakkers SHM, Vullev VI, Morikis D. Discovery of Small Molecules for Fluorescent Detection of Complement Activation Product C3d. J Med Chem 2015; 58:9535-45. [DOI: 10.1021/acs.jmedchem.5b01062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ronald D. Gorham
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
- Department
of Medical Microbiology, University Medical Center, Utrecht, 3584 CX Utrecht, The Netherlands
| | - Vicente Nuñez
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - Jung-Hsin Lin
- Division
of Mechanics,
Research Center for Applied Sciences and Institute of Biomedical Sciences,
Academia Sinica, Taipei 115, Taiwan
- School
of Pharmacy, National Taiwan University, Taipei 100, Taiwan
| | - Suzan H. M. Rooijakkers
- Department
of Medical Microbiology, University Medical Center, Utrecht, 3584 CX Utrecht, The Netherlands
| | - Valentine I. Vullev
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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10
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Melillo D, Varriale S, Giacomelli S, Natale L, Bargelloni L, Oreste U, Pinto MR, Coscia MR. Evolution of the complement system C3 gene in Antarctic teleosts. Mol Immunol 2015; 66:299-309. [PMID: 25909494 DOI: 10.1016/j.molimm.2015.03.247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 11/29/2022]
Abstract
Notothenioidei are typical Antarctic teleosts evolved to adapt to the very low temperatures of the Antarctic seas. Aim of the present paper is to investigate sequence and structure of C3, the third component of the complement system of the notothenioid Trematomus bernacchii and Chionodraco hamatus. We determined the complete nucleotide sequence of two C3 isoforms of T. bernacchii and a single C3 isoform of C. hamatus. These sequences were aligned against other homologous teleost sequences to check for the presence of diversifying selection. Evidence for positive selection was observed in the evolutionary lineage of Antarctic teleost C3 sequences, especially in that of C. hamatus, the most recently diverged species. Adaptive selection affected numerous amino acid positions including three residues located in the anaphylatoxin domain. In an attempt to evaluate the link between sequence variants and specific structural features, we constructed molecular models of Antarctic teleost C3s, of their proteolytic fragments C3b and C3a, and of the corresponding molecules of the phylogenetically related temperate species Epinephelus coioides, using human crystallographic structures as templates. Subsequently, we compared dynamic features of these models by molecular dynamics simulations and found that the Antarctic C3s models show higher flexibility, which likely allows for more pronounced movements of both the TED domain in C3b and the carboxyl-terminal region of C3a. As such dynamic features are associated to positively selected sites, it appears that Antarctic teleost C3 molecules positively evolved toward an increased flexibility, to cope with low kinetic energy levels of the Antarctic marine environment.
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Affiliation(s)
- Daniela Melillo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli (SZN), Italy
| | - Sonia Varriale
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Stefano Giacomelli
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Lenina Natale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli (SZN), Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padua, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Umberto Oreste
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Maria Rosaria Pinto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli (SZN), Italy
| | - Maria Rosaria Coscia
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
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11
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E S Harrison R, Gorham RD, Morikis D. Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex. Protein Sci 2015; 24:789-802. [PMID: 25628052 DOI: 10.1002/pro.2650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/27/2014] [Accepted: 01/25/2015] [Indexed: 01/01/2023]
Abstract
As a part of innate immunity, the complement system relies on activation of the alternative pathway (AP). While feed-forward amplification generates an immune response towards foreign surfaces, the process requires regulation to prevent an immune response on the surface of host cells. Factor H (FH) is a complement protein secreted by native cells to negatively regulate the AP. In terms of structure, FH is composed of 20 complement-control protein (CCP) modules that are structurally homologous but vary in composition and function. Mutations in these CCPs have been linked to states of autoimmunity. In particular, several mutations in CCP 19-20 are correlated to atypical hemolytic uremic syndrome (aHUS). From crystallographic structures there are three putative binding sites of CCP 19-20 on C3d. Since there has been some controversy over the primary mode of binding from experimental studies, we approach characterization of binding using computational methods. Specifically, we compare each binding mode in terms of electrostatic character, structural stability, dissociative and associative properties, and predicted free energy of binding. After a detailed investigation, we found two of the three binding sites to be similarly stable while varying in the number of contacts to C3d and in the energetic barrier to complex dissociation. These sites are likely physiologically relevant and may facilitate multivalent binding of FH CCP 19-20 to C3b and either C3d or host glycosaminoglycans. We propose thermodynamically stable binding with modules 19 and 20, the latter driven by electrostatics, acting synergistically to increase the apparent affinity of FH for host surfaces.
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Affiliation(s)
- Reed E S Harrison
- Department of Bioengineering, Bourns College of Engineering, University of California, Riverside, California
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