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S Al-Otaibi J, Mary YS, Mary YS, Thomas R. Evidence of cluster formation of croconic acid with Ag, Au and Cu cages, enhancement of electronic properties and Raman activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120233. [PMID: 34358780 DOI: 10.1016/j.saa.2021.120233] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Investigation of the adsorption properties croconic acid (CCA) with metal clusters (mC: Ag, Au and Cu) are reported using DFT method. CCA is found to form stable cluster with transition metal clusters of copper, silver and gold. The drug-cluster complexaton energy is slightly more for the copper nanocluster-drug complex. Non-covalent interaction analysis indicated that strong interactions and weak van der Waal interaction is present between drug and metal clusters. Dipole moment of the drug-gold cluster is found to be higher than that of the other systems. SERS studies demonstrates improved Raman signals for multiple wavenumbers of all CCA-metal cluster complexes. Mulliken charge analysis show that all CCA oxygen atom's charge changes due to the interactions with the mCs. Clustering of CCA with metal cages enhances the medicinal properties and the metal nanoclusters will act as a drug carrier of CCA.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | | | | | - Renjith Thomas
- Deparment of Chemsitry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
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2
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Abdizadeh H, Jalalypour F, Atilgan AR, Atilgan C. A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs. Front Mol Biosci 2020; 7:210. [PMID: 33195399 PMCID: PMC7477071 DOI: 10.3389/fmolb.2020.00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 11/13/2022] Open
Abstract
We address the problem of triggering dissociation events between proteins that have formed a complex. We have collected a set of 25 non-redundant, functionally diverse protein complexes having high-resolution three-dimensional structures in both the unbound and bound forms. We unify elastic network models with perturbation response scanning (PRS) methodology as an efficient approach for predicting residues that have the propensity to trigger dissociation of an interacting protein pair, using the three-dimensional structures of the bound and unbound proteins as input. PRS reveals that while for a group of protein pairs, residues involved in the conformational shifts are confined to regions with large motions, there are others where they originate from parts of the protein unaffected structurally by binding. Strikingly, only a few of the complexes have interface residues responsible for dissociation. We find two main modes of response: In one mode, remote control of dissociation in which disruption of the electrostatic potential distribution along protein surfaces play the major role; in the alternative mode, mechanical control of dissociation by remote residues prevail. In the former, dissociation is triggered by changes in the local environment of the protein, e.g., pH or ionic strength, while in the latter, specific perturbations arriving at the controlling residues, e.g., via binding to a third interacting partner is required for decomplexation. We resolve the observations by relying on an electromechanical coupling model which reduces to the usual elastic network result in the limit of the lack of coupling. We validate the approach by illustrating the biological significance of top residues selected by PRS on select cases where we show that the residues whose perturbation leads to the observed conformational changes correspond to either functionally important or highly conserved residues in the complex.
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Affiliation(s)
- Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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3
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Hemmadi V, Biswas M. An overview of moonlighting proteins in Staphylococcus aureus infection. Arch Microbiol 2020; 203:481-498. [PMID: 33048189 PMCID: PMC7551524 DOI: 10.1007/s00203-020-02071-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Staphylococcus aureus is responsible for numerous instances of superficial, toxin-mediated, and invasive infections. The emergence of methicillin-resistant (MRSA), as well as vancomycin-resistant (VRSA) strains of S. aureus, poses a massive threat to human health. The tenacity of S. aureus to acquire resistance against numerous antibiotics in a very short duration makes the effort towards developing new antibiotics almost futile. S. aureus owes its destructive pathogenicity to the plethora of virulent factors it produces among which a majority of them are moonlighting proteins. Moonlighting proteins are the multifunctional proteins in which a single protein, with different oligomeric conformations, perform multiple independent functions in different cell compartments. Peculiarly, proteins involved in key ancestral functions and metabolic pathways typically exhibit moonlighting functions. Pathogens mainly employ those proteins as virulent factors which exhibit high structural conservation towards their host counterparts. Consequentially, the host immune system counteracts these invading bacterial virulent factors with minimal protective action. Additionally, many moonlighting proteins also play multiple roles in various stages of pathogenicity while augmenting the virulence of the bacterium. This has necessitated elaborative studies to be conducted on moonlighting proteins of S. aureus that can serve as drug targets. This review is a small effort towards understanding the role of various moonlighting proteins in the pathogenicity of S. aureus.
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Affiliation(s)
- Vijay Hemmadi
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India
| | - Malabika Biswas
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India.
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4
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Weng G, Wang E, Wang Z, Liu H, Zhu F, Li D, Hou T. HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Res 2020; 47:W322-W330. [PMID: 31106357 PMCID: PMC6602443 DOI: 10.1093/nar/gkz397] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) play an important role in the different functions of cells, but accurate prediction of the three-dimensional structures for PPIs is still a notoriously difficult task. In this study, HawkDock, a free and open accessed web server, was developed to predict and analyze the structures of PPIs. In the HawkDock server, the ATTRACT docking algorithm, the HawkRank scoring function developed in our group and the MM/GBSA free energy decomposition analysis were seamlessly integrated into a multi-functional platform. The structures of PPIs were predicted by combining the ATTRACT docking and the HawkRank re-scoring, and the key residues for PPIs were highlighted by the MM/GBSA free energy decomposition. The molecular visualization was supported by 3Dmol.js. For the structural modeling of PPIs, HawkDock could achieve a better performance than ZDOCK 3.0.2 in the benchmark testing. For the prediction of key residues, the important residues that play an essential role in PPIs could be identified in the top 10 residues for ∼81.4% predicted models and ∼95.4% crystal structures in the benchmark dataset. To sum up, the HawkDock server is a powerful tool to predict the binding structures and identify the key residues of PPIs. The HawkDock server is accessible free of charge at http://cadd.zju.edu.cn/hawkdock/.
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Affiliation(s)
- Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Zhu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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5
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Giussani S, Pietrocola G, Donnarumma D, Norais N, Speziale P, Fabbrini M, Margarit I. The Streptococcus agalactiae complement interfering protein combines multiple complement-inhibitory mechanisms by interacting with both C4 and C3 ligands. FASEB J 2018; 33:4448-4457. [PMID: 30566365 PMCID: PMC6404586 DOI: 10.1096/fj.201801991r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Group B Streptococcus (GBS) colonizes the human lower intestinal and genital tracts and constitutes a major threat to neonates from pregnant carrier mothers and to adults with underlying morbidity. The pathogen expresses cell-surface virulence factors that enable cell adhesion and penetration and that counteract innate and adaptive immune responses. Among these, the complement interfering protein (CIP) was recently described for its capacity to interact with the human C4b ligand and to interfere with the classical- and lectin-complement pathways. In the present study, we provide evidence that CIP can also interact with C3, C3b, and C3d. Immunoassay-based competition experiments showed that binding of CIP to C3d interferes with the interaction between C3d and the complement receptor 2/cluster of differentiation 21 (CR2/CD21) receptor on B cells. By B-cell intracellular signaling assays, CIP was confirmed to down-regulate CR2/CD21-dependent B-cell activation. The CIP domain involved in C3d binding was mapped via hydrogen deuterium exchange–mass spectrometry. The data obtained reveal a new role for this GBS polypeptide at the interface between the innate and adaptive immune responses, adding a new member to the growing list of virulence factors secreted by gram-positive pathogens that incorporate multiple immunomodulatory functions.—Giussani, S., Pietrocola, G., Donnarumma, D., Norais, N., Speziale, P., Fabbrini, M., Margarit, I. The Streptococcus agalactiae complement interfering protein combines multiple complement-inhibitory mechanisms by interacting with both C4 and C3 ligands.
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Affiliation(s)
- Stefania Giussani
- GlaxoSmithKline (GSK), Siena, Italy; and.,Unit of Biochemistry, Molecular Medicine Department, University of Pavia, Pavia, Italy
| | - Giampiero Pietrocola
- Unit of Biochemistry, Molecular Medicine Department, University of Pavia, Pavia, Italy
| | | | | | - Pietro Speziale
- Unit of Biochemistry, Molecular Medicine Department, University of Pavia, Pavia, Italy
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6
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Devaurs D, Papanastasiou M, Antunes DA, Abella JR, Moll M, Ricklin D, Lambris JD, Kavraki LE. Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling. INTERNATIONAL JOURNAL OF COMPUTATIONAL BIOLOGY AND DRUG DESIGN 2018; 11:90-113. [PMID: 30700993 PMCID: PMC6349257 DOI: 10.1504/ijcbdd.2018.090834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen/deuterium exchange detected by mass spectrometry (HDXMS) provides valuable information on protein structure and dynamics. Although HDX-MS data is often interpreted using crystal structures, it was suggested that conformational ensembles produced by molecular dynamics simulations yield more accurate interpretations. In this paper, we analyse the complement protein C3d by performing an HDX-MS experiment, and evaluate several interpretation methodologies using an existing prediction model to derive HDX-MS data from protein structure. To interpret and refine C3d's HDX-MS data, we look for a conformation (or conformational ensemble) of C3d that allows computationally replicating this data. We confirm that crystal structures are not a good choice and suggest that conformational ensembles produced by molecular dynamics simulations might not always be satisfactory either. Finally, we show that coarse-grained conformational sampling of C3d produces a conformation from which its HDX-MS data can be replicated and refined.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Dinler A Antunes
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Mark Moll
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
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7
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Papanastasiou M, Koutsogiannaki S, Sarigiannis Y, Geisbrecht BV, Ricklin D, Lambris JD. Structural Implications for the Formation and Function of the Complement Effector Protein iC3b. THE JOURNAL OF IMMUNOLOGY 2017; 198:3326-3335. [PMID: 28258193 DOI: 10.4049/jimmunol.1601864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/10/2017] [Indexed: 01/17/2023]
Abstract
Complement-mediated opsonization, phagocytosis, and immune stimulation are critical processes in host defense and homeostasis, with the complement activation fragment iC3b playing a key effector role. To date, however, there is no high-resolution structure of iC3b, and some aspects of its structure-activity profile remain controversial. Here, we employed hydrogen-deuterium exchange mass spectrometry to describe the structure and dynamics of iC3b at a peptide resolution level in direct comparison with its parent protein C3b. In our hydrogen-deuterium exchange mass spectrometry study, 264 peptides were analyzed for their deuterium content, providing almost complete sequence coverage for this 173-kDa protein. Several peptides in iC3b showed significantly higher deuterium uptake when compared with C3b, revealing more dynamic, solvent-exposed regions. Most of them resided in the CUB domain, which contains the heptadecapeptide C3f that is liberated during the conversion of C3b to iC3b. Our data suggest a highly disordered CUB, which has acquired a state similar to that of intrinsically disordered proteins, resulting in a predominant form of iC3b that features high structural flexibility. The structure was further validated using an anti-iC3b mAb that was shown to target an epitope in the CUB region. The information obtained in this work allows us to elucidate determinants of iC3b specificity and activity and provide functional insights into the protein's recognition pattern with respect to regulators and receptors of the complement system.
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Affiliation(s)
- Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Sophia Koutsogiannaki
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Yiannis Sarigiannis
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
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8
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Naudin C, Schumski A, Salo-Ahen OMH, Herwald H, Smeds E. A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo. Microb Biotechnol 2017; 10:657-665. [PMID: 28168836 PMCID: PMC5404189 DOI: 10.1111/1751-7915.12601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/15/2016] [Indexed: 12/01/2022] Open
Abstract
Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well‐characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA‐based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost‐effective method that can be used to prevent unnecessary animal experiments.
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Affiliation(s)
- Clément Naudin
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Ariane Schumski
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Outi M H Salo-Ahen
- Faculty of Natural Sciences and Engineering, Pharmacy, Åbo Akademi University, Turku, Finland
| | - Heiko Herwald
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Emanuel Smeds
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
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9
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Ricklin D, Reis ES, Mastellos DC, Gros P, Lambris JD. Complement component C3 - The "Swiss Army Knife" of innate immunity and host defense. Immunol Rev 2016; 274:33-58. [PMID: 27782325 PMCID: PMC5427221 DOI: 10.1111/imr.12500] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As a preformed defense system, complement faces a delicate challenge in providing an immediate, forceful response to pathogens even at first encounter, while sparing host cells in the process. For this purpose, it engages a tightly regulated network of plasma proteins, cell surface receptors, and regulators. Complement component C3 plays a particularly versatile role in this process by keeping the cascade alert, acting as a point of convergence of activation pathways, fueling the amplification of the complement response, exerting direct effector functions, and helping to coordinate downstream immune responses. In recent years, it has become evident that nature engages the power of C3 not only to clear pathogens but also for a variety of homeostatic processes ranging from tissue regeneration and synapse pruning to clearing debris and controlling tumor cell progression. At the same time, its central position in immune surveillance makes C3 a target for microbial immune evasion and, if improperly engaged, a trigger point for various clinical conditions. In our review, we look at the versatile roles and evolutionary journey of C3, discuss new insights into the molecular basis for C3 function, provide examples of disease involvement, and summarize the emerging potential of C3 as a therapeutic target.
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Affiliation(s)
- Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Edimara S Reis
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitrios C Mastellos
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- National Center for Scientific Research 'Demokritos', Athens, Greece
| | - Piet Gros
- Utrecht University, Utrecht, The Netherlands
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Petrauskas V, Maximowitsch E, Matulis D. Thermodynamics of Ion Pair Formations Between Charged Poly(Amino Acid)s. J Phys Chem B 2015; 119:12164-71. [PMID: 26317887 DOI: 10.1021/acs.jpcb.5b05767] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Electrostatic interactions between the positively and negatively charged amino acids in proteins play an important role in macromolecular stability, binding, and recognition. Numerous amino acids in proteins are ionizable and may exist in negatively (e.g., Glu, Asp, Cys, Tyr) or positively (e.g., Arg, Lys, His, Orn) charged form dependent on pH and their pKas. In this work, isothermal titration calorimetry was used to determine the average standard values of thermodynamic parameters (the Gibbs free energy, enthalpy, entropy, and the heat capacity) of interaction between the positively charged amino acid homopolymers (polyarginine, polylysine, and polyornithine) and the negatively charged homopolymers (polyaspartic and polyglutamic acids). These values are of potential use in the computational models of interacting proteins and other biological macromolecules. The study showed that oppositely charged poly(amino acid)s bound each other with the stoichiometry of one positive to one negative charge. Arginine bound to the negatively charged amino acids with exothermic enthalpy and higher affinity than lysine. This result also suggests that positive charges in proteins should not be considered entirely equivalent if carried by lysine or arginine. The difference in binding energy of arginine and lysine association with the negatively charged amino acids was attributed to the enthalpy of the second ionic hydrogen bond formation between the guanidine and carboxylic groups. Despite the favorable enthalpic contribution, all such ion pair formation reactions were largely entropy-driven. Consistent with previously observed ionic interactions, the positive heat capacity was always observed during the amino acid ion pair formation.
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Affiliation(s)
- Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
| | - Eglė Maximowitsch
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, LT-02241 Vilnius, Lithuania
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12
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Merle NS, Noe R, Halbwachs-Mecarelli L, Fremeaux-Bacchi V, Roumenina LT. Complement System Part II: Role in Immunity. Front Immunol 2015; 6:257. [PMID: 26074922 PMCID: PMC4443744 DOI: 10.3389/fimmu.2015.00257] [Citation(s) in RCA: 655] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/09/2015] [Indexed: 12/14/2022] Open
Abstract
The complement system has been considered for a long time as a simple lytic cascade, aimed to kill bacteria infecting the host organism. Nowadays, this vision has changed and it is well accepted that complement is a complex innate immune surveillance system, playing a key role in host homeostasis, inflammation, and in the defense against pathogens. This review discusses recent advances in the understanding of the role of complement in physiology and pathology. It starts with a description of complement contribution to the normal physiology (homeostasis) of a healthy organism, including the silent clearance of apoptotic cells and maintenance of cell survival. In pathology, complement can be a friend or a foe. It acts as a friend in the defense against pathogens, by inducing opsonization and a direct killing by C5b–9 membrane attack complex and by triggering inflammatory responses with the anaphylatoxins C3a and C5a. Opsonization plays also a major role in the mounting of an adaptive immune response, involving antigen presenting cells, T-, and B-lymphocytes. Nevertheless, it can be also an enemy, when pathogens hijack complement regulators to protect themselves from the immune system. Inadequate complement activation becomes a disease cause, as in atypical hemolytic uremic syndrome, C3 glomerulopathies, and systemic lupus erythematosus. Age-related macular degeneration and cancer will be described as examples showing that complement contributes to a large variety of conditions, far exceeding the classical examples of diseases associated with complement deficiencies. Finally, we discuss complement as a therapeutic target.
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Affiliation(s)
- Nicolas S Merle
- UMRS 1138, Centre de Recherche des Cordeliers, INSERM , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Paris Cité, Université Paris Descartes , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Universités, UPMC Université Paris 06 , Paris , France
| | - Remi Noe
- UMRS 1138, Centre de Recherche des Cordeliers, INSERM , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Paris Cité, Université Paris Descartes , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Universités, UPMC Université Paris 06 , Paris , France ; Ecole Pratique des Hautes Études (EPHE) , Paris , France
| | - Lise Halbwachs-Mecarelli
- UMRS 1138, Centre de Recherche des Cordeliers, INSERM , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Paris Cité, Université Paris Descartes , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Universités, UPMC Université Paris 06 , Paris , France
| | - Veronique Fremeaux-Bacchi
- UMRS 1138, Centre de Recherche des Cordeliers, INSERM , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Paris Cité, Université Paris Descartes , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Universités, UPMC Université Paris 06 , Paris , France ; Service d'Immunologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges-Pompidou , Paris , France
| | - Lubka T Roumenina
- UMRS 1138, Centre de Recherche des Cordeliers, INSERM , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Paris Cité, Université Paris Descartes , Paris , France ; UMRS 1138, Centre de Recherche des Cordeliers, Sorbonne Universités, UPMC Université Paris 06 , Paris , France
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13
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Yugandhar K, Gromiha MM. Protein–protein binding affinity prediction from amino acid sequence. Bioinformatics 2014; 30:3583-9. [DOI: 10.1093/bioinformatics/btu580] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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14
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García-Machorro J, López-González M, Barrios-Rojas O, Fernández-Pomares C, Sandoval-Montes C, Santos-Argumedo L, Villegas-Sepúlveda N, Gutiérrez-Castañeda B, Cedillo-Barrón L. DENV-2 subunit proteins fused to CR2 receptor-binding domain (P28)-induces specific and neutralizing antibodies to the Dengue virus in mice. Hum Vaccin Immunother 2013; 9:2326-35. [PMID: 23880886 DOI: 10.4161/hv.25673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Domain III (DIII) of the dengue virus (DENV) envelope (E) protein induces strong neutralizing type-specific antibodies. In addition, a region near the fusion loop in domain II (DII) induces the production of cross-reactive antibodies with neutralizing potential. Thus, this study aimed to generate DENV-2 recombinant fusion proteins (i.e., rEII*EIII and rEII*EIII/NS1*) either alone or fused to 3 copies of P28, the minimum CR2-binding domain of the complement protein C3d. The 4 recombinant proteins were generated in a Drosophila melanogaster Schneider 2 (S2) cell system. The expression and secretion of the recombinant proteins were confirmed in vitro using immunofluorescence (IF) and western blot (WB) analyses. Human dengue immune serum samples recognized recombinant proteins. The immunogenicity of the 4 proteins in BALB/c mice was analyzed using ELISA, and the results revealed that the induced specific antibody response was higher in the groups of mice immunized with the P28 fusion proteins. Interestingly, although the 4 recombinant proteins were able to elicit high levels of neutralizing antibodies in BALB/c mice; no adjuvant effect was observed in terms of neutralizing antibodies in the groups immunized with proteins containing P28. Thus, ELISA and PRNT50 assays may evaluate different epitopes and responses, where ELISA showed a wider response that did not always correlate with neutralization. Furthermore, the elicited antibodies were able to recognize the immobilized E glycoprotein of DENV. All mice vaccinated with the DENV-2 recombinant proteins showed induction of higher levels of IgG1 antibodies than of IgG2a antibodies.
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Affiliation(s)
- Jazmín García-Machorro
- Department of Molecular Biomedicine Centre for Research and Advanced Studies (CINVESTAV-IPN) Av. IPN # 2508 Col.; San Pedro Zacatenco, D.F. Mexico, Mexico
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15
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Ricklin D. Manipulating the mediator: modulation of the alternative complement pathway C3 convertase in health, disease and therapy. Immunobiology 2013; 217:1057-66. [PMID: 22964231 DOI: 10.1016/j.imbio.2012.07.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 10/27/2022]
Abstract
The complement network is increasingly recognized as an important triage system that is able to differentiate between healthy host cells, microbial intruders, cellular debris and immune complexes, and tailor its actions accordingly. At the center of this triage mechanism is the alternative pathway C3 convertase (C3bBb), a potent enzymatic protein complex capable of rapidly converting the inert yet abundant component C3 into powerful effector fragments (C3a and C3b), thereby amplifying the initial response on unprotected surfaces and inducing a variety of effector functions. A fascinating molecular mechanism of convertase assembly and intrinsic regulation, as well as the interplay with a panel of cell surface-bound and soluble inhibitors are essential for directing complement attack to intruders and protecting healthy host cells. While efficiently keeping immune surveillance and homeostasis on track, the reliance on an intricate cascade of interaction and conversion steps also renders the C3 convertase vulnerable to derail. On the one hand, tissue damage, accumulation of debris, or polymorphisms in complement genes may unfavorably shift the balance between activation and regulation, thereby contributing to a variety of clinical conditions. On the other hand, pathogens developed powerful evasion strategies to avoid complement attack by targeting the convertase. Finally, we increasingly challenge our bodies with foreign materials such as biomaterial implants or drug delivery vehicles that may induce adverse effects that are at least partially caused by complement activation and amplification via the alternative pathway. The involvement of the C3 convertase in a range of pathological conditions put this complex into the spotlight of complement-targeted drug discovery efforts. Fortunately, the physiological regulation and microbial evasion approaches provide a rich source of inspiration for the development of powerful treatment options. This review provides insight into the current knowledge about the molecular mechanisms that drive C3 convertase activity, reveals common and divergent strategies of convertase inhibition employed by host and pathogens, and how this inhibitory arsenal can be tapped for developing therapeutic options to treat complement-related diseases.
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Affiliation(s)
- Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia 19104, USA.
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16
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Koch TK, Reuter M, Barthel D, Böhm S, van den Elsen J, Kraiczy P, Zipfel PF, Skerka C. Staphylococcus aureus proteins Sbi and Efb recruit human plasmin to degrade complement C3 and C3b. PLoS One 2012; 7:e47638. [PMID: 23071827 PMCID: PMC3469469 DOI: 10.1371/journal.pone.0047638] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/13/2012] [Indexed: 11/19/2022] Open
Abstract
Upon host infection, the human pathogenic microbe Staphylococcus aureus (S. aureus) immediately faces innate immune reactions such as the activated complement system. Here, a novel innate immune evasion strategy of S. aureus is described. The staphylococcal proteins surface immunoglobulin-binding protein (Sbi) and extracellular fibrinogen-binding protein (Efb) bind C3/C3b simultaneously with plasminogen. Bound plasminogen is converted by bacterial activator staphylokinase or by host-specific urokinase-type plasminogen activator to plasmin, which in turn leads to degradation of complement C3 and C3b. Efb and to a lesser extend Sbi enhance plasmin cleavage of C3/C3b, an effect which is explained by a conformational change in C3/C3b induced by Sbi and Efb. Furthermore, bound plasmin also degrades C3a, which exerts anaphylatoxic and antimicrobial activities. Thus, S. aureus Sbi and Efb comprise platforms to recruit plasmin(ogen) together with C3 and its activation product C3b for efficient degradation of these complement components in the local microbial environment and to protect S. aureus from host innate immune reactions.
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Affiliation(s)
- Tina K. Koch
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
| | - Michael Reuter
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
| | - Diana Barthel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
| | - Sascha Böhm
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
| | | | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Germany
| | - Peter F. Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
- Friedrich Schiller University Jena, Germany
| | - Christine Skerka
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection, Biology, Jena, Germany
- * E-mail:
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17
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Moal IH, Fernández-Recio J. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. ACTA ACUST UNITED AC 2012; 28:2600-7. [PMID: 22859501 DOI: 10.1093/bioinformatics/bts489] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MOTIVATION Empirical models for the prediction of how changes in sequence alter protein-protein binding kinetics and thermodynamics can garner insights into many aspects of molecular biology. However, such models require empirical training data and proper validation before they can be widely applied. Previous databases contained few stabilizing mutations and no discussion of their inherent biases or how this impacts model construction or validation. RESULTS We present SKEMPI, a database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein-protein heterodimeric complexes with experimentally determined structures. This represents over four times more data than previously collected. Changes in 713 association and dissociation rates and 127 enthalpies and entropies were also recorded. The existence of biases towards specific mutations, residues, interfaces, proteins and protein families is discussed in the context of how the data can be used to construct predictive models. Finally, a cross-validation scheme is presented which is capable of estimating the efficacy of derived models on future data in which these biases are not present. AVAILABILITY The database is available online at http://life.bsc.es/pid/mutation_database/.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, Spain
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18
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Garcia BL, Ramyar KX, Ricklin D, Lambris JD, Geisbrecht BV. Advances in understanding the structure, function, and mechanism of the SCIN and Efb families of Staphylococcal immune evasion proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 946:113-33. [PMID: 21948365 DOI: 10.1007/978-1-4614-0106-3_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Our understanding of both the nature and diversity of Staphylococcal immune evasion proteins has increased tremendously throughout the last several years. Among this group of molecules, members of the SCIN and Efb families of complement inhibitors have been the subject of particularly intense study. This work has demonstrated that both types of proteins exert their primary function by inhibiting C3 convertases, which lie at the heart of the complement-mediated immune response. Despite this similarity, however, significant differences in structure/function relationships and mechanisms of action exist between these bacterial proteins. Furthermore, divergent secondary effects on host immune responses have also been described for these two protein families. This chapter summarizes recent advances toward understanding the structure, function, and mechanism of the SCIN and Efb families, and suggests potential directions for the field over the coming years.
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Affiliation(s)
- Brandon L Garcia
- School of Biological Sciences, University of Missouri, Kansas City, MO 64110, USA.
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19
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Complement Inhibition by Staphylococcus aureus: Electrostatics of C3d–EfbC and C3d–Ehp Association. Cell Mol Bioeng 2011. [DOI: 10.1007/s12195-011-0195-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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20
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Chikalov I, Yao P, Moshkov M, Latombe JC. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories. BMC Bioinformatics 2011; 12 Suppl 1:S34. [PMID: 21342565 PMCID: PMC3044290 DOI: 10.1186/1471-2105-12-s1-s34] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Methods This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration Δ. We model dependence of the output variable on the predictors by a regression tree. Results Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings. Conclusions We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone.
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Affiliation(s)
- Igor Chikalov
- Mathematical and Computer Sciences & Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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21
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Clark EA, Crennell S, Upadhyay A, Zozulya AV, Mackay JD, Svergun DI, Bagby S, van den Elsen JM. A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d. Mol Immunol 2011; 48:452-62. [PMID: 21055811 PMCID: PMC3025320 DOI: 10.1016/j.molimm.2010.09.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/28/2010] [Accepted: 09/30/2010] [Indexed: 01/07/2023]
Abstract
The structure of the complement-binding domain of Staphylococcus aureus protein Sbi (Sbi-IV) in complex with ligand C3d is presented. The 1.7Å resolution structure reveals the molecular details of the recognition of thioester-containing fragment C3d of the central complement component C3, involving interactions between residues of Sbi-IV helix α2 and the acidic concave surface of C3d. The complex provides a structural basis for the binding preference of Sbi for native C3 over C3b and explains how Sbi-IV inhibits the interaction between C3d and complement receptor 2. A second C3d binding site on Sbi-IV is identified in the crystal structure that is not observed in related S. aureus C3 inhibitors Efb-C and Ehp. This binding mode perhaps hints as to how Sbi-IV, as part of Sbi, forms a C3b-Sbi adduct and causes futile consumption of C3, an extraordinary aspect of Sbi function that is not shared by any other known Staphylococcal complement inhibitor.
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Affiliation(s)
- Elizabeth A. Clark
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Susan Crennell
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Abhishek Upadhyay
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | | | - Julia D. Mackay
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | | | - Stefan Bagby
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Jean M.H. van den Elsen
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom,Corresponding author. Tel.: +44 1225 383639; fax: +44 1225 386779.
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22
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Allosteric inhibition of complement function by a staphylococcal immune evasion protein. Proc Natl Acad Sci U S A 2010; 107:17621-6. [PMID: 20876141 DOI: 10.1073/pnas.1003750107] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The complement system is a major target of immune evasion by Staphylococcus aureus. Although many evasion proteins have been described, little is known about their molecular mechanisms of action. Here we demonstrate that the extracellular fibrinogen-binding protein (Efb) from S. aureus acts as an allosteric inhibitor by inducing conformational changes in complement fragment C3b that propagate across several domains and influence functional regions far distant from the Efb binding site. Most notably, the inhibitor impaired the interaction of C3b with complement factor B and, consequently, formation of the active C3 convertase. As this enzyme complex is critical for both activation and amplification of the complement response, its allosteric inhibition likely represents a fundamental contribution to the overall immune evasion strategy of S. aureus.
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23
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Haspel N, Geisbrecht BV, Lambris J, Kavraki L. Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex. Proteins 2010; 78:1004-14. [PMID: 19899169 DOI: 10.1002/prot.22624] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present a novel multi-level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi-scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low-dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra-cellular fibrinogen-binding domain (Efb-C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
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24
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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25
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Ricklin D, Tzekou A, Garcia BL, Hammel M, McWhorter WJ, Sfyroera G, Wu YQ, Holers VM, Herbert AP, Barlow PN, Geisbrecht BV, Lambris JD. A molecular insight into complement evasion by the staphylococcal complement inhibitor protein family. THE JOURNAL OF IMMUNOLOGY 2009; 183:2565-74. [PMID: 19625656 DOI: 10.4049/jimmunol.0901443] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Staphylococcus aureus possesses an impressive arsenal of complement evasion proteins that help the bacterium escape attack of the immune system. The staphylococcal complement inhibitor (SCIN) protein exhibits a particularly high potency and was previously shown to block complement by acting at the level of the C3 convertases. However, many details about the exact binding and inhibitory mechanism remained unclear. In this study, we demonstrate that SCIN directly binds with nanomolar affinity to a functionally important area of C3b that lies near the C terminus of its beta-chain. Direct competition of SCIN with factor B for C3b slightly decreased the formation of surface-bound convertase. However, the main inhibitory effect can be attributed to an entrapment of the assembled convertase in an inactive state. Whereas native C3 is still able to bind to the blocked convertase, no generation and deposition of C3b could be detected in the presence of SCIN. Furthermore, SCIN strongly competes with the binding of factor H to C3b and influences its regulatory activities: the SCIN-stabilized convertase was essentially insensitive to decay acceleration by factor H and the factor I- and H-mediated conversion of surface-bound C3b to iC3b was significantly reduced. By targeting a key area on C3b, SCIN is able to block several essential functions within the alternative pathway, which explains the high potency of the inhibitor. Our findings provide an important insight into complement evasion strategies by S. aureus and may act as a base for further functional studies.
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Affiliation(s)
- Daniel Ricklin
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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26
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Ricklin D, Ricklin-Lichtsteiner SK, Markiewski MM, Geisbrecht BV, Lambris JD. Cutting edge: members of the Staphylococcus aureus extracellular fibrinogen-binding protein family inhibit the interaction of C3d with complement receptor 2. THE JOURNAL OF IMMUNOLOGY 2008; 181:7463-7. [PMID: 19017934 DOI: 10.4049/jimmunol.181.11.7463] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Staphylococcus aureus expresses a highly diversified arsenal of immune evasion proteins, many of which target the complement system. The extracellular fibrinogen-binding protein (Efb) and the Efb homologous protein (Ehp) have previously been demonstrated to bind to C3 and inhibit complement activation and amplification. In this study we present the first evidence that Efb and Ehp are also capable of inhibiting the interaction of C3d with complement receptor 2 (CR2), which plays an important role in B cell activation and maturation. The C-terminal domain of Efb efficiently blocked this interaction both in surface plasmon resonance-based competition studies and cellular assays and prevented the CR2-mediated stimulation of B cells. Furthermore, analyses of the available structural data were consistent with a molecular mechanism that reflects both steric and electrostatic effects on the C3d-CR2 interaction. Our study therefore suggests that S. aureus may disrupt both the innate and adaptive immune responses with a single protein module.
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Affiliation(s)
- Daniel Ricklin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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