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Harwood SJ, Smith CR, Lawson JD, Ketcham JM. Selected Approaches to Disrupting Protein-Protein Interactions within the MAPK/RAS Pathway. Int J Mol Sci 2023; 24:ijms24087373. [PMID: 37108538 PMCID: PMC10139024 DOI: 10.3390/ijms24087373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Within the MAPK/RAS pathway, there exists a plethora of protein-protein interactions (PPIs). For many years, scientists have focused efforts on drugging KRAS and its effectors in hopes to provide much needed therapies for patients with KRAS-mutant driven cancers. In this review, we focus on recent strategies to inhibit RAS-signaling via disrupting PPIs associated with SOS1, RAF, PDEδ, Grb2, and RAS.
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Affiliation(s)
| | | | - J David Lawson
- Mirati Therapeutics, 3545 Cray Court, San Diego, CA 92121, USA
| | - John M Ketcham
- Mirati Therapeutics, 3545 Cray Court, San Diego, CA 92121, USA
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2
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Han Y, He F, Chen Y, Qin W, Yu H, Xu D. Quality Assessment of Protein Docking Models Based on Graph Neural Network. FRONTIERS IN BIOINFORMATICS 2021; 1:693211. [PMID: 36303780 PMCID: PMC9581034 DOI: 10.3389/fbinf.2021.693211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022] Open
Abstract
Protein docking provides a structural basis for the design of drugs and vaccines. Among the processes of protein docking, quality assessment (QA) is utilized to pick near-native models from numerous protein docking candidate conformations, and it directly determines the final docking results. Although extensive efforts have been made to improve QA accuracy, it is still the bottleneck of current protein docking systems. In this paper, we presented a Deep Graph Attention Neural Network (DGANN) to evaluate and rank protein docking candidate models. DGANN learns inter-residue physio-chemical properties and structural fitness across the two protein monomers in a docking model and generates their probabilities of near-native models. On the ZDOCK decoy benchmark, our DGANN outperformed the ranking provided by ZDOCK in terms of ranking good models into the top selections. Furthermore, we conducted comparative experiments on an independent testing dataset, and the results also demonstrated the superiority and generalization of our proposed method.
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Affiliation(s)
- Ye Han
- School of Information Technology, Jilin Agricultural University, Changchun, China
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Fei He
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Yongbing Chen
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Wenyuan Qin
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Helong Yu
- School of Information Technology, Jilin Agricultural University, Changchun, China
- *Correspondence: Helong Yu, ; Dong Xu,
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- *Correspondence: Helong Yu, ; Dong Xu,
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3
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Jin SC, Kim MH, Choi LY, Nam YK, Yang WM. Fat regulatory mechanisms of pine nut oil based on protein interaction network analysis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 86:153557. [PMID: 33852976 DOI: 10.1016/j.phymed.2021.153557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Pine nut oil (PNO), a standardized and well-defined extract of Pinus koraiensis (Korean pine), has beneficial effects on wound healing, inflammatory diseases, and cancer. However, the explanation for the mechanism by which PNO reduces body fat remains uncertain. We performed a protein-protein interaction network (PPIN) analysis to explore the genes associated with pinolenic acid using the MEDILINE database from PubChem and PubMed. It was concluded through the PPIN analysis that PNO was involved in a neutral lipid biosynthetic process. PURPOSE This study evaluated the effects of PNO predicted by the network analysis of fat accumulation in chronic obesity mouse models established by feeding a high fat diet (HFD) to C57BL/6J mice and explored potential mechanisms. METHODS HFD mice were fed only HFD or HFD with PNO at 822 and 1644 mg/kg. After an oral administration of 7 weeks, several body weight and body fat-related parameters were examined, including the following: adipose weight, adipocyte size, serum lipid profiles, adipocyte expression of PPAR-γ, sterol regulatory element binding protein (SREBP)-1c, lipoprotein lipase (LPL) and leptin. RESULTS We showed that oral administration of PNO to HFD mice reduces body fat weight, fat in tissue, white adipose tissue weight, and adipocyte size. The serum cholesterol was improved in the HFD mice treated with PNO. Additionally, PNO has significantly attenuated the HFD-induced changes in the adipose tissue expression of PPAR-γ, SREBP-1c, LPL, and leptin. CONCLUSIONS The findings from this study based on the PPIN analysis suggest that PNO has potential as drug to reduce body fat through fat regulatory mechanisms by PPAR-γ and SREBP-1c.
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Affiliation(s)
- Seong Chul Jin
- Department of Convergence Korean Medical Science, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi Hye Kim
- Department of Convergence Korean Medical Science, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - La Yoon Choi
- Department of Convergence Korean Medical Science, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yeon Kyung Nam
- Department of Convergence Korean Medical Science, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Woong Mo Yang
- Department of Convergence Korean Medical Science, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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4
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Kowalski A. A survey of human histone H1 subtypes interaction networks: Implications for histones H1 functioning. Proteins 2021; 89:792-810. [PMID: 33550666 DOI: 10.1002/prot.26059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/23/2020] [Accepted: 01/31/2021] [Indexed: 11/08/2022]
Abstract
To show a spectrum of histone H1 subtypes (H1.1-H1.5) activity realized through the protein-protein interactions, data selected from APID resources were processed with sequence-based bioinformatics approaches. Histone H1 subtypes participate in over half a thousand interactions with nuclear and cytosolic proteins (ComPPI database) engaged in the enzymatic activity and binding of nucleic acids and proteins (SIFTER tool). Small-scale networks of H1 subtypes (STRING network) have similar topological parameters (P > .05) which are, however, different for networks hubs between subtype H1.1 and H1.4 and subtype H1.3 and H1.5 (P < .05) (Cytoscape software). Based on enriched GO terms (g:Profiler toolset) of interacting proteins, molecular function and biological process of networks hubs is related to RNA binding and ribosome biogenesis (subtype H1.1 and H1.4), cell cycle and cell division (subtype H1.3 and H1.5) and protein ubiquitination and degradation (subtype H1.2). The residue propensity (BIPSPI predictor) and secondary structures of interacting surfaces (GOR algorithm) as well as a value of equilibrium dissociation constant (ISLAND predictor) indicate that a type of H1 subtypes interactions is transient in term of the stability and medium-strong in relation to the strength of binding. Histone H1 subtypes bind interacting partners in the intrinsic disorder-dependent mode (FoldIndex, PrDOS predictor), according to the coupled folding and binding and mutual synergistic folding mechanism. These results evidence that multifunctional H1 subtypes operate via protein interactions in the networks of crucial cellular processes and, therefore, confirm a new histone H1 paradigm relating to its functioning in the protein-protein interaction networks.
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Affiliation(s)
- Andrzej Kowalski
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University in Kielce, Kielce, Poland
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5
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Prestel A, Wichmann N, Martins JM, Marabini R, Kassem N, Broendum SS, Otterlei M, Nielsen O, Willemoës M, Ploug M, Boomsma W, Kragelund BB. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cell Mol Life Sci 2019; 76:4923-4943. [PMID: 31134302 PMCID: PMC6881253 DOI: 10.1007/s00018-019-03150-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/16/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a potential drug target. Its binding partners carry a short linear motif (SLiM) known as the PCNA-interacting protein-box (PIP-box), but sequence-divergent motifs have been reported to bind to the same binding pocket. To investigate how PCNA accommodates motif diversity, we assembled a set of 77 experimentally confirmed PCNA-binding proteins and analyzed features underlying their binding affinity. Combining NMR spectroscopy, affinity measurements and computational analyses, we corroborate that most PCNA-binding motifs reside in intrinsically disordered regions, that structure preformation is unrelated to affinity, and that the sequence-patterns that encode binding affinity extend substantially beyond the boundaries of the PIP-box. Our systematic multidisciplinary approach expands current views on PCNA interactions and reveals that the PIP-box affinity can be modulated over four orders of magnitude by positive charges in the flanking regions. Including the flanking regions as part of the motif is expected to have broad implications, particularly for interpretation of disease-causing mutations and drug-design, targeting DNA-replication and -repair.
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Affiliation(s)
- Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Nanna Wichmann
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Joao M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Riccardo Marabini
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Noah Kassem
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian S Broendum
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, 3800, Australia
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Olaf Nielsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Finsen Laboratory, Biotechnology Research Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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6
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Yang W, Sun X, Zhang C, Lai L. Discovery of novel helix binding sites at protein-protein interfaces. Comput Struct Biotechnol J 2019; 17:1396-1403. [PMID: 31768230 PMCID: PMC6872852 DOI: 10.1016/j.csbj.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023] Open
Abstract
Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding site, which has limited the applications of protein-protein interface binding peptide design. Here, we developed a general computational algorithm, HPer (Helix Positioner), that locates single-helix binding sites at protein-protein interfaces based on the structure of protein targets. HPer performed well on known single-helix-mediated PPIs and recaptured the key interactions and hot-spot residues of native helical binders. We also screened non-helical-mediated PPIs in the PDBbind database and identified 17 PPIs that were suitable for helical peptide binding, and the helical binding sites in these PPIs were also predicted for designing novel peptide ligands. The L2 domain of EGFR, which was the top ranked, was selected as an example to show the protocol and results of designing novel helical peptide ligands on the searched binding site. The binding stability of the designed sequences were further investigated using molecular dynamics simulations.
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Affiliation(s)
- Wei Yang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Xiangyu Sun
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changsheng Zhang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, AAIS, Peking University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
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7
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A large-scale comparative analysis of affinity, thermodynamics and functional characteristics of interactions of twelve cytochrome P450 isoforms and their redox partners. Biochimie 2019; 162:156-166. [DOI: 10.1016/j.biochi.2019.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/24/2019] [Indexed: 12/16/2022]
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8
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhsky LA, Florinskaya AV, Buneeva OA, Medvedev AE, Ivanov AS. Effect of Bioregulator Isatin on Protein–Protein Interactions Involving Isatin-Binding Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018010053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Akiba H, Tsumoto K. Thermodynamics of antibody–antigen interaction revealed by mutation analysis of antibody variable regions. ACTA ACUST UNITED AC 2015; 158:1-13. [DOI: 10.1093/jb/mvv049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/11/2015] [Indexed: 01/20/2023]
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10
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Lagunin A, Druzhilovsky D, Rudik A, Filimonov D, Gawande D, Suresh K, Goel R, Poroikov V. Computer evaluation of hidden potential of phytochemicals of medicinal plants of the traditional indian ayurvedic medicine. ACTA ACUST UNITED AC 2015; 61:286-97. [DOI: 10.18097/pbmc20156102286] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Applicability of our computer programs PASS and PharmaExpert to prediction of biological activity spectra of rather complex and structurally diverse phytocomponents of medicinal plants, both separately and in combinations has been evaluated. The web-resource on phytochemicals of 50 medicinal plants used in Ayurveda was created for the study of hidden therapeutic potential of Traditional Indian Medicine (TIM) (http://ayurveda.pharmaexpert.ru). It contains information on 50 medicinal plants, their using in TIM and their pharmacology activities, also as 1906 phytocomponents. PASS training set was updated by addition of information about 946 natural compounds; then the training procedure and validation were performed, to estimate the quality of PASS prediction. It was shown that the difference between the average accuracy of prediction obtained in leave-5%-out cross-validation (94,467%) and in leave-one-out cross-validation (94,605%) is very small. These results showed high predictive ability of the program. Results of biological activity spectra prediction for all phytocomponents included in our database are in good correspondence with the experimental data. Additional kinds of biological activity predicted with high probability provide the information about most promising directions of further studies. The analysis of prediction results of sets of phytocomponents in each of 50 medicinal plants was made by PharmaExpert software. Based on this analysis, we found that the combination of phytocomponents from Passiflora incarnata may exhibit nootropic, anticonvulsant and antidepressant effects. Experiments carried out in mice models confirmed the predicted effects of Passiflora incarnata extracts.
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Affiliation(s)
- A.A. Lagunin
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - A.V. Rudik
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - D. Gawande
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala-147002 India
| | - K. Suresh
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala-147002 India
| | - R. Goel
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala-147002 India
| | - V.V. Poroikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Nirantar SR, Li X, Siau JW, Ghadessy FJ. Rapid screening of protein–protein interaction inhibitors using the protease exclusion assay. Biosens Bioelectron 2014; 56:250-7. [DOI: 10.1016/j.bios.2013.12.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/13/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
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12
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Ivanov AS, Ershov PV, Poverennaya EV, Lisitsa AV, Archakov AI. [Protocols of proteins interactomics: molecular fishing on optical chips and magnetic nanoparticles]. BIOMEDITSINSKAIA KHIMIIA 2013; 59:171-182. [PMID: 23789344 DOI: 10.18097/pbmc20135902171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Now it is absolutely clear, that the majority of proteins in living systems function due to interaction with each other in stable or dynamic proteins complexes. Therefore necessity of deeper studies of proteins functions causes expansion of protein-protein interaction research. In the present review the brief description and comparative estimation of experimental methods and protocols of protein interactomics, based on technology of molecular fishing on an optical chips and paramagnetic nanoparticles is given.
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13
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Effect of dimerization on the catalytic properties of native and chimeric organophosphorus hydrolase determined by molecular modeling of the enzyme structure. Russ Chem Bull 2012. [DOI: 10.1007/s11172-012-0062-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Ershov P, Mezentsev Y, Gnedenko O, Mukha D, Yantsevich A, Britikov V, Kaluzhskiy L, Yablokov E, Molnar A, Ivanov A, Lisitsa A, Gilep A, Usanov S, Archakov A. Protein interactomics based on direct molecular fishing on paramagnetic particles: experimental simulation and SPR validation. Proteomics 2012; 12:3295-8. [PMID: 23001861 DOI: 10.1002/pmic.201200135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 07/04/2012] [Accepted: 08/14/2012] [Indexed: 11/10/2022]
Abstract
We describe an experimental approach for direct molecular fishing of prey protein on the surface of two types of paramagnetic particles (PMP) having different size and composition. Human microsomal cytochrome b(5) (b(5)) and its known partner human cytochrome P450 3A5 (CYP3A5) were used as bait and prey proteins, respectively. For assessing the level of unspecific binding of background proteins, α-fetoprotein (aFP) was used. SPR measurements were applied for quantitative analysis of trapped proteins (CYP3A5 and aFP) after fishing on PMP. It was shown that the described approach of molecular fishing on micro-PMP provides enough prey proteins for LC-MS/MS identification and SPR validation, so this approach can be used for discovery of new protein-protein interactions in the framework of Human Proteome Project.
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Affiliation(s)
- Pavel Ershov
- Orechovich Institute of Biomedical Chemistry of RAMS, Moscow, Russia
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15
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Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev Mol Med 2012; 14:e16. [PMID: 22831787 DOI: 10.1017/erm.2012.10] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, might influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of 'druggable' protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favour discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets.
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16
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Ivanov AS, Ershov PV, Mezentsev YV, Poverennaya EV, Lisitsa AV, Archakov AI. Protocols of protein interactomics: Molecular fishing on optical chips and magnetic nanoparticles. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2012. [DOI: 10.1134/s1990750812020072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Ivanov AS, Gnedenko OV, Molnar AA, Mezentsev YV, Lisitsa AV, Archakov AI. PROTEIN–PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: VIRTUAL AND EXPERIMENTAL APPROACHES. J Bioinform Comput Biol 2011; 5:579-92. [PMID: 17636863 DOI: 10.1142/s0219720007002825] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/18/2022]
Abstract
Protein–protein and protein–ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein–protein interactions (PPI) is very important for basic-, as well as applied research. The interface areas of protein complexes have unique structure and properties, so PPI represent prospective targets for a new generation of drugs. One of the key targets of PPI inhibitors are oligomeric enzymes. This report shows interactive links between virtual and experimental approaches in a total pipeline "from gene to drug" and using Surface Plasmon Resonance technology for experimentally assessing PPI. Our research is conducted on two oligomeric enzymes — HIV-1 protease (HIVp) (homo-dimer) and bacterial L-asparaginase (homo-tetramer). Using methods of molecular modeling and computational alanine scanning we obtained structural and functional description of PPI in these two enzymes. We also presented a real example of application of integral approach in searching inhibitors of HIVp dimerization — from virtual database mining up to experimental testing of lead compounds.
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Affiliation(s)
- Alexis S Ivanov
- V.N.Orechovich Institute of Biomedical Chemistry RAMS, Pogodinskaya str. 10, Moscow, 119121, Russia.
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18
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Bustos DM. The role of protein disorder in the 14-3-3 interaction network. MOLECULAR BIOSYSTEMS 2011; 8:178-84. [PMID: 21947246 DOI: 10.1039/c1mb05216k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Disordered regions are segments of a protein that do not fold completely and thus remain flexible. These regions have key physiological roles, particularly in phospho-proteins, which are enriched in disorder-promoting residues surrounding their phosphorylation sites. 14-3-3 proteins are ordered hubs that interact with multiple and diverse intrinsically disordered phosphorylated targets. This provides 14-3-3 with the ability to participate in and to regulate multiple signalling networks. Here, I review the effect of structural disorder on the mechanism involved in 14-3-3 protein-protein interactions and how 14-3-3 impacts cell biology through disordered ligands. How 14-3-3 proteins constitute an advantageous system to identify novel classes of biological tools is discussed with a special emphasis on a particular-and innovative-use of small molecules to stabilize 14-3-3 protein complexes, useful to study gene expression, cancer signalling and neurodegenerative diseases.
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Affiliation(s)
- Diego M Bustos
- Instituto Tecnológico de Chascomús (IIB-INTECH, CONICET-UNSAM), Chascomús, Argentina.
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19
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Kaĭsheva AL, Ivanov ID, Zgoda VG, Frantsuzov PA, Pleshakova TO, Krokhin NV, Ziborov VS, Archakov AI. [Visualization and identification of hepatitis C viral particles by atomic force microscopy combined with MS/MS analysis]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2011; 56:26-39. [PMID: 21328909 DOI: 10.18097/pbmc20105601026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Possibility of detection and identification of hepatitis C viral particles with mass spectrometry (MS) in combination with atomic force microscopy (AFM) had been investigated. AFM/MS approach is based on two technologies: (1) AFM-biospecific fishing that allows to detect, concentrate from solution and to count protein complexes on a surface of AFM-nanochip; (2) mass spectrometric identification of these complexes. AFM-biospecific fishing of HCVcoreAg from solution was carried onto surface of AFM-nanochips with immobilized anti-HCVcoreAg. It was shown that HCVcoreAg/anti-HCVcore(im) complexes were formed onto AFM-nanochips in quantity sufficient for mass spectrometric identification. Thus, AFM/MS approach allows to identify fragments of hepatitis C virus fished onto a surface of AFM-nanochip from serum.
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20
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Kubala MH, Kovtun O, Alexandrov K, Collins BM. Structural and thermodynamic analysis of the GFP:GFP-nanobody complex. Protein Sci 2011; 19:2389-401. [PMID: 20945358 DOI: 10.1002/pro.519] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The green fluorescent protein (GFP)-nanobody is a single-chain VHH antibody domain developed with specific binding activity against GFP and is emerging as a powerful tool for isolation and cellular engineering of fluorescent protein fusions in many different fields of biological research. Using X-ray crystallography and isothermal titration calorimetry, we determine the molecular details of GFP:GFP-nanobody complex formation and explain the basis of high affinity and at the same time high specificity of protein binding. Although the GFP-nanobody can also bind YFP, it cannot bind the closely related CFP or other fluorescent proteins from the mFruit series. CFP differs from GFP only within the central chromophore and at one surface amino acid position, which lies in the binding interface. Using this information, we have engineered a CFP variant (I146N) that is also able to bind the GFP-nanobody with high affinity, thus extending the toolbox of genetically encoded fluorescent probes that can be isolated using the GFP-nanobody.
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Affiliation(s)
- Marta H Kubala
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
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Ivanov AS, Zgoda VG, Archakov AI. Technologies of protein interactomics: A review. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:8-21. [DOI: 10.1134/s1068162011010092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Archakov AI, Ivanov YD. Application of AFM and optical biosensor for investigation of complexes formed in P450-containing monooxygenase systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:102-10. [PMID: 20832504 DOI: 10.1016/j.bbapap.2010.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/20/2010] [Accepted: 08/29/2010] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) allows to visualize and count the individual protein molecules and their complexes within multiprotein systems. On the other hand, optical biosensor (OB) provides information on complex formation kinetics as well as complex lifetime (τ(LT)) and affinity. Comparison of complex lifetime τ(LT) with the time required for enzyme's catalytic cycle (τ(cat)) enables to characterize productive complexes and distinguish them from non-productive ones. Both these approaches were applied for the analysis of the three cytochrome P450-containing monooxygenase systems: cytochrome P450 101, cytochrome P450 11A1 and cytochrome P450 2B4. By using AFM, the formation of binary and ternary protein complexes was registered in all the three systems. OB analysis enabled to kinetically characterize these binary and ternary complexes. It was shown that the binary complexes putidaredoxin reductase (PdR)/putidaredoxin (Pd) and Pd/cytochrome P450 101 (P450 101) formed within the P450 101 system and, also, the binary complexes adrenodoxin reductase (AdR)/adrenodoxin (Ad) and Ad/cytochrome P450 11A1 (P450 11A1) formed within the P450 11A1 system are non-productive (deadlock). At the same time, the ternary PdR/Pd/P450 101 and AdR/Ad/P450 11A1 complexes proved to be productive. The binary cytochrome P450 reductase (Fp)/cytochrome P450 2B4 (2B4) complexes and the ternary Fp/2B4/cytochrome b5 (b5) complexes formed within P450 2B4 system were productive.
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Affiliation(s)
- A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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23
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Sigalov AB. The SCHOOL of nature: III. From mechanistic understanding to novel therapies. SELF/NONSELF 2010; 1:192-224. [PMID: 21487477 PMCID: PMC3047783 DOI: 10.4161/self.1.3.12794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 11/19/2022]
Abstract
Protein-protein interactions play a central role in biological processes and thus represent an appealing target for innovative drug design and development. They can be targeted by small molecule inhibitors, modulatory peptides and peptidomimetics, which represent a superior alternative to protein therapeutics that carry many disadvantages. Considering that transmembrane signal transduction is an attractive process to therapeutically control multiple diseases, it is fundamentally and clinically important to mechanistically understand how signal transduction occurs. Uncovering specific protein-protein interactions critical for signal transduction, a general platform for receptor-mediated signaling, the signaling chain homooligomerization (SCHOOL) platform, suggests these interactions as universal therapeutic targets. Within the platform, the general principles of signaling are similar for a variety of functionally unrelated receptors. This suggests that global therapeutic strategies targeting key protein-protein interactions involved in receptor triggering and transmembrane signal transduction may be used to treat a diverse set of diseases. This also assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T cell-mediated skin diseases and platelet disorders or combined to develop novel pharmacological approaches. Intriguingly, human viruses use the SCHOOL-like strategies to modulate and/or escape the host immune response. These viral mechanisms are highly optimized over the millennia, and the lessons learned from viral pathogenesis can be used practically for rational drug design. Proof of the SCHOOL concept in the development of novel therapies for atopic dermatitis, rheumatoid arthritis, cancer, platelet disorders and other multiple indications with unmet needs opens new horizons in therapeutics.
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24
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Selective adsorption of small proteins on large-pore anion exchangers coated with medium size proteins. Colloids Surf B Biointerfaces 2010; 78:140-5. [DOI: 10.1016/j.colsurfb.2010.02.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 02/24/2010] [Accepted: 02/26/2010] [Indexed: 11/21/2022]
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25
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Yu Z, Cui M, Yan C, Song F, Liu Z, Liu S, Zhang H. Gas phase isomeric differentiation of oleanolic and ursolic acids associated with heptakis-(2,6-di-O-methyl)-beta-cyclodextrin by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:444-50. [PMID: 20306522 DOI: 10.1002/jms.1733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Oleanolic acid (OA) and ursolic acid (UA) are isomeric triterpenoid compounds with similar pharmaceutical properties. Usually, modern chromatographic and electrophoretic methods are widely utilized to differentiate these two compounds. Compared with mass spectrometric (MS) methods, these modern separation methods are both time- and sample-consuming. Herein, we present a new method for structural differentiation of OA and UA by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with the association of heptakis-(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD). Exact MS and tandem MS (MS/MS) data showed that there is no perceptible difference between OA and UA, as well as their beta-cyclodextrin and gamma-cyclodextrin complexes. However, there is a remarkable difference in MS/MS spectra of DM-beta-CD complexes of OA and UA. The peak corresponding to the neutral loss of a formic acid and a water molecule could only be observed in the MS/MS spectrum of the complex of DM-beta-CD : OA. Molecular modeling calculations were also employed to further investigate the structural differences of DM-beta-CD : OA and DM-beta-CD : UA complexes. Therefore, by employing DM-beta-CD as a reference reagent, OA and UA could be differentiated with purely MS method.
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Affiliation(s)
- Zhan Yu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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26
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The DraC usher in Dr fimbriae biogenesis of uropathogenic E. coli Dr+ strains. Arch Microbiol 2010; 192:351-63. [DOI: 10.1007/s00203-010-0564-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 02/12/2010] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
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27
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Kaysheva AL, Ivanov YD, Zgoda VG, Frantsuzov PA, Pleshakova TO, Krokhin NV, Ziborov VS, Archakov AI. Visualization and identification of hepatitis C viral particles by atomic force microscopy combined with MS/MS analysis. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2010. [DOI: 10.1134/s1990750810010038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Sigalov AB. The SCHOOL of nature: I. Transmembrane signaling. SELF/NONSELF 2010; 1:4-39. [PMID: 21559175 PMCID: PMC3091606 DOI: 10.4161/self.1.1.10832] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 11/30/2009] [Accepted: 12/01/2009] [Indexed: 11/19/2022]
Abstract
Receptor-mediated transmembrane signaling plays an important role in health and disease. Recent significant advances in our understanding of the molecular mechanisms linking ligand binding to receptor activation revealed previously unrecognized striking similarities in the basic structural principles of function of numerous cell surface receptors. In this work, I demonstrate that the Signaling Chain Homooligomerization (SCHOOL)-based mechanism represents a general biological mechanism of transmembrane signal transduction mediated by a variety of functionally unrelated single- and multichain activating receptors. within the SCHOOL platform, ligand binding-induced receptor clustering is translated across the membrane into protein oligomerization in cytoplasmic milieu. This platform resolves a long-standing puzzle in transmembrane signal transduction and reveals the major driving forces coupling recognition and activation functions at the level of protein-protein interactions-biochemical processes that can be influenced and controlled. The basic principles of transmembrane signaling learned from the SCHOOL model can be used in different fields of immunology, virology, molecular and cell biology and others to describe, explain and predict various phenomena and processes mediated by a variety of functionally diverse and unrelated receptors. Beyond providing novel perspectives for fundamental research, the platform opens new avenues for drug discovery and development.
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Affiliation(s)
- Alexander B Sigalov
- Department of Pathology; University of Massachusetts Medical School; Worcester, MA USA
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29
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Mahon E, Aastrup T, Barboiu M. Dynamic glycovesicle systems for amplified QCM detection of carbohydrate-lectin multivalent biorecognition. Chem Commun (Camb) 2010; 46:2441-3. [DOI: 10.1039/b924766a] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Chitta RK, Rempel DL, Gross ML. The gramicidin dimer shows both EX1 and EX2 mechanisms of H/D exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1813-1820. [PMID: 19631556 PMCID: PMC2767204 DOI: 10.1016/j.jasms.2009.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 05/08/2009] [Accepted: 05/28/2009] [Indexed: 05/28/2023]
Abstract
We describe the use of H/D amide exchange and electrospray ionization mass spectrometry to study, in organic solvents, the pentadecapeptide gramicidin as a model for protein self association. In methanol-OD, all active H's in the peptide exchange for D within 5 min, indicating a monomer/dimer equilibrium that is shifted towards the fast-exchanging monomer. H/D exchange in n-propanol-OD, however, showed a partially protected gramicidin that slowly converts to a second species that exchanges nearly all the active hydrogens, indicating EX1 kinetics for the H/D exchange. We propose that this behavior is the result of the slower rate of unfolding in n-propanol compared with that in methanol. The rate constant for the unfolding of the dimer is the rate of disappearance of the partially protected species, and it agrees within a factor of two with a value reported in literature. The rate constant of dimer refolding can be determined from the ratio of the rate constant for unfolding and the affinity constant for the dimer, which we determined in an earlier study. The unfolding activation energy is 20 kcal mol(-1), determined by performing the exchange experiments as a function of temperature. To study gramicidin in an even more hydrophobic medium than n-propanol, we measured its H/D exchange kinetics in a phospholipids vesicle and found a different H/D amide exchange behavior. Gramicidin is an unusual peptide dimer that can exhibit both EX1 and EX2 mechanisms for its H/D exchange, depending on the solvent.
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Affiliation(s)
- Raghu K Chitta
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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31
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Ershov PV, Gnedenko OV, Molnar AA, Lisitsa AV, Ivanov AS, Archakov AI. Biosensor analysis of the interaction of potential dimerization inhibitors with HIV-1 protease. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2009. [DOI: 10.1134/s199075080903007x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Gordo S, Giralt E. Knitting and untying the protein network: modulation of protein ensembles as a therapeutic strategy. Protein Sci 2009; 18:481-93. [PMID: 19241367 DOI: 10.1002/pro.43] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteins constitute the working machinery and structural support of all organisms. In performing a given function, they must adopt highly specific structures that can change with their level of activity, often through the direct or indirect action of other proteins. Indeed, proteins typically function within an ensemble, rather than individually. Hence, they must be sufficiently flexible to interact with each other and execute diverse tasks. The discovery that errors within these groups can ultimately cause disease has led to a paradigm shift in drug discovery, from an emphasis on single protein targets to a holistic approach whereby entire ensembles are targeted.
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Affiliation(s)
- Susana Gordo
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
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33
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Lawrence HR, Li Z, Yip MR, Sung SS, Lawrence NJ, McLaughlin ML, McManus GJ, Zaworotko MJ, Sebti SM, Chen J, Guida WC. Identification of a disruptor of the MDM2-p53 protein-protein interaction facilitated by high-throughput in silico docking. Bioorg Med Chem Lett 2009; 19:3756-9. [PMID: 19457663 PMCID: PMC2754843 DOI: 10.1016/j.bmcl.2009.04.124] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/24/2009] [Accepted: 04/24/2009] [Indexed: 11/29/2022]
Abstract
NSC 333003 has been identified from the NCI Diversity Set as an inhibitor of the MDM2-p53 protein-protein interaction by in silico docking (virtual screening). Its potency and chemical characteristics render it well suited for lead optimization studies that can result in more potent analogs with improved drug-like properties. Its synthesis was achieved using an acid catalyzed condensation reaction from commercially available benzothiazole hydrazine and pyridyl phenyl ketone in refluxing methanol. Stereochemical implications for this compound are described.
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Affiliation(s)
- Harshani R. Lawrence
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- High-throughput Screening and Chemistry Core, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
| | - Zhenyu Li
- Molecular Oncology Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
| | - M.L. Richard Yip
- High-throughput Screening and Chemistry Core, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
| | - Shen-Shu Sung
- High-throughput Screening and Chemistry Core, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
| | - Nicholas J. Lawrence
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620
| | - Mark L. McLaughlin
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620
- Department of Chemistry, University of South Florida, Tampa, FL 33620
| | | | | | - Saïd M. Sebti
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620
| | - Jiandong Chen
- Molecular Oncology Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620
| | - Wayne C. Guida
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- High-throughput Screening and Chemistry Core, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620
- Department of Chemistry, University of South Florida, Tampa, FL 33620
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Zhang B, Xing Y, Li Z, Zhou H, Mu Q, Yan B. Functionalized carbon nanotubes specifically bind to alpha-chymotrypsin's catalytic site and regulate its enzymatic function. NANO LETTERS 2009; 9:2280-4. [PMID: 19408924 PMCID: PMC2814308 DOI: 10.1021/nl900437n] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Although carbon nanotubes (CNTs) have been shown to nonspecifically bind proteins through charge complementary, pi-pi stacking or hydrophobic interactions, they have not been shown to bind to a specific site on proteins. By generating surface molecular diversity, we created functionalized CNTs that recognize and bind to the catalytic site of alpha-chymotrypsin and inhibit its enzymatic activity competitively.
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Affiliation(s)
- Bin Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
| | - Yuehan Xing
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
| | - Zhenwei Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
| | - Hongyu Zhou
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
- St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - Qingxin Mu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
- St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
| | - Bing Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, China, 250100
- St. Jude Children’s Research Hospital, Memphis, Tennessee 38105
- Corresponding author: To whom correspondence should be addressed. Phone: +9014952797. Fax: +9014955715.
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35
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Heredia KL, Grover GN, Tao L, Maynard HD. Synthesis of Heterotelechelic Polymers for Conjugation of Two Different Proteins. Macromolecules 2009; 42:2360-2367. [PMID: 25378715 DOI: 10.1021/ma8022712] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report we describe a straightforward approach to synthesize polymers with end-groups that bind site-specifically to two different proteins. Telechelic biotin, maleimide poly(N-isopropylacrylamide) (pNIPAAm) was synthesized for the formation of streptavidin (SAv)-bovine serum albumin (BSA) polymer conjugates. Reversible addition-fragmentation chain transfer (RAFT) polymerization of NIPAAm was conducted in the presence of biotinylated chain transfer agents (CTAs) with either ester or amide linkages, and the resultant α-biotinylated pNIPAAm were formed with low polydispersity indices (PDI ≤ 1.09). UV-Vis analysis of the trithiocarbonate chain-ends indicated 88% or greater retention of the group. A maleimide was introduced to the ω chain-end via a radical cross-coupling reaction with a functionalized azo-initiator. The polymer structures were characterized by 1H NMR spectroscopy and gel permeation chromatography (GPC). The resultant biotin-maleimide heterotelechelic polymer was used to form a SAv-BSA heterodimer conjugate. Bioconjugate formation was confirmed by gel electrophoresis.
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Affiliation(s)
- Karina L Heredia
- Department of Chemistry and Biochemistry and the California NanoSystems Institute University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569
| | - Gregory N Grover
- Department of Chemistry and Biochemistry and the California NanoSystems Institute University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569
| | - Lei Tao
- Department of Chemistry and Biochemistry and the California NanoSystems Institute University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569
| | - Heather D Maynard
- Department of Chemistry and Biochemistry and the California NanoSystems Institute University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569
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36
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Axarli I, Dhavala P, Papageorgiou AC, Labrou NE. Crystallographic and functional characterization of the fluorodifen-inducible glutathione transferase from Glycine max reveals an active site topography suited for diphenylether herbicides and a novel L-site. J Mol Biol 2009; 385:984-1002. [PMID: 19014949 DOI: 10.1016/j.jmb.2008.10.084] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 10/24/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Glutathione transferases (GSTs) from the tau class (GSTU) are unique to plants and have important roles in stress tolerance and the detoxification of herbicides in crops and weeds. A fluorodifen-induced GST isoezyme (GmGSTU4-4) belonging to the tau class was purified from Glycine max by affinity chromatography. This isoenzyme was cloned and expressed in Escherichia coli, and its structural and catalytic properties were investigated. The structure of GmGSTU4-4 was determined at 1.75 A resolution in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH). The enzyme adopts the canonical GST fold but with a number of functionally important differences. Compared with other plant GSTs, the three-dimensional structure of GmGSTU4-4 primarily shows structural differences in the hydrophobic substrate binding site, the linker segment and the C-terminal region. The X-ray structure identifies key amino acid residues in the hydrophobic binding site (H-site) and provides insights into the substrate specificity and catalytic mechanism of the enzyme. The isoenzyme was highly active in conjugating the diphenylether herbicide fluorodifen. A possible reaction pathway involving the conjugation of glutathione with fluorodifen is described based on site-directed mutagenesis and molecular modeling studies. A serine residue (Ser13) is present in the active site, at a position that would allow it to stabilise the thiolate anion of glutathione and enhance its nucleophilicity. Tyr107 and Arg111 present in the active site are important structural moieties that modulate the catalytic efficiency and specificity of the enzyme, and participate in k(cat) regulation by affecting the rate-limiting step of the catalytic reaction. A hitherto undescribed ligand-binding site (L-site) located in a surface pocket of the enzyme was also found. This site is formed by conserved residues, suggesting it may have an important functional role in the transfer and delivery of bound ligands, presumably to specific protein receptors.
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Affiliation(s)
- Irene Axarli
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855-Athens, Greece
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37
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Kiewitz SD, Kruppa M, Riechers A, König B, Cabrele C. Recognition of the helix-loop-helix domain of the Id proteins by an artificial luminescent metal complex receptor. J Mol Recognit 2008; 21:79-88. [PMID: 18383104 DOI: 10.1002/jmr.872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Synthetic agents specifically interacting with a protein interface are important not only for the better understanding of protein dimer or complex formation but also for medical applications. Here we describe the recognition of the helix-loop-helix (HLH) dimerization domain of the Id proteins by an artificial luminescent receptor containing two binding sites for a Lewis acid and a Lewis base, respectively. The Id proteins are inhibitors of bHLH transcription factors and play key roles during development of cancer. We show that a receptor/Id-HLH-domain complex was formed cooperatively (K(0.5) approximately 2 microM under physiological conditions) and with moderate specificity, as compared to the related MyoD and Max HLH domains. Accordingly, a preferred receptor binding motif, CYSR(K), was identified within the Id HLH domains. These results are promising and may be exploited to design highly selective synthetic receptors for the Id HLH domain.
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Affiliation(s)
- Sebastian D Kiewitz
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
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38
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Friedman S, Kolusheva S, Volinsky R, Zeiri L, Schrader T, Jelinek R. Lipid/Polydiacetylene Films for Colorimetric Protein Surface-Charge Analysis. Anal Chem 2008; 80:7804-11. [DOI: 10.1021/ac801254v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sarit Friedman
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Sofiya Kolusheva
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Roman Volinsky
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Leila Zeiri
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Thomas Schrader
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Raz Jelinek
- Department of Chemistry and Ilse Katz Institute for Nanotechnology, Ben Gurion University, Beer Sheva, Israel 84105, and Institute of Organic Chemistry, Universität Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
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Abstract
Protein-protein interactions play a central role in biological processes and thus are an appealing target for innovative drug design a nd development. They can be targeted bysmall molecule inhibitors, peptides and peptidomimetics, which represent an alternative to protein therapeutics that carry many disadvantages. In this chapter, I describe specific protein-protein interactions suggested by a novel model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, to be critical for cell activation mediated by multichain immune recognition receptors (MIRRs) expressed on different cells of the hematopoietic system. Unraveling a long-standing mystery of MIRR triggering and transmembrane signaling, the SCHOOL model reveals the intrareceptor transmembrane interactions and interreceptor cytoplasmic homointeractions as universal therapeutic targets for a diverse variety of disorders mediated by immune cells. Further, assuming that the general principles underlying MIRR-mediated transmembrane signaling mechanisms are similar, the SCHOOL model can be applied to any particular receptor of the MIRR family. Thus, an important application of the SCHOOL model is that global therapeutic strategies targeting key protein-protein interactions involved in MIRR triggering and transmembrane signal transduction may be used to treat a diverse set of immune-mediated diseases. This assumes that clinical knowledge and therapeutic strategies can be transferred between seemingly disparate disorders, such as T-cell-mediated skin diseases and platelet disorders, or combined to develop novel pharmacological approaches. Intriguingly, the SCHOOL model unravels the molecular mechanisms underlying ability of different human viruses such as human immunodeficiency virus, cytomegalovirus and severe acute respiratory syndrome coronavirus to modulate and/or escape the host immune response. It also demonstrates how the lessons learned from viral pathogenesis can be used practically for rational drug design. Application of this model to platelet collagen receptor signaling has already led to the development of a novel concept of platelet inhibition and the invention of new platelet inhibitors, thus proving the suggested hypothesis and highlighting the importance and broad perspectives of the SCHOOL model in the development of new targeting strategies.
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Sugita T, Yoshikawa T, Mukai Y, Yamanada N, Imai S, Nagano K, Yoshida Y, Shibata H, Yoshioka Y, Nakagawa S, Kamada H, Tsunoda SI, Tsutsumi Y. Improved cytosolic translocation and tumor-killing activity of Tat-shepherdin conjugates mediated by co-treatment with Tat-fused endosome-disruptive HA2 peptide. Biochem Biophys Res Commun 2007; 363:1027-32. [DOI: 10.1016/j.bbrc.2007.09.077] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 09/14/2007] [Indexed: 12/18/2022]
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Schweigert FJ. Nutritional Proteomics: Methods and Concepts for Research in Nutritional Science. ANNALS OF NUTRITION AND METABOLISM 2007; 51:99-107. [PMID: 17476098 DOI: 10.1159/000102101] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nutritional proteomics or nutriproteomics is the application of proteomics methodology to nutrition-related research but also represents the interaction of bioactive food ingredients with proteins, whereby the interaction with proteins occurs in two basically specific ways. Firstly, the effect of nutrients on protein expression, which can be monitored by protein mapping, and secondly, the interaction of nutrients with proteins by post-translational modifications or small-molecule protein interactions. These interactions result in changes to the three-dimensional structure of such effected proteins. As a consequence, their original functions are modulated, resulting for example in reduced activity in the case of enzymes or changes in ability of recognition between molecules such as protein-protein interactions and ligand-receptor interactions. The characterization of such modifications together with functional data from established biochemical and physiological methods will result in a better understanding of the interplay between bioactive dietary components and diet-related diseases such as cancer, diabetes or neurodegenerative diseases. The occurrence of such modifications can possibly be additionally used as biomarkers in the diagnosis and therapy of these diseases as well as biomarkers for the efficacy or safety of selected nutrients.
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Affiliation(s)
- Florian J Schweigert
- Department of Physiology and Pathophysiology, Institute of Nutritional Science, University of Potsdam, Potsdam-Rehbrücke, Germany.
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Fuentes M, Mateo C, Pessela BCC, Batalla P, Fernandez-Lafuente R, Guisán JM. Solid phase proteomics: Dramatic reinforcement of very weak protein–protein interactions. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:243-50. [PMID: 17035103 DOI: 10.1016/j.jchromb.2006.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 09/14/2006] [Accepted: 09/18/2006] [Indexed: 11/19/2022]
Abstract
Very weak protein-protein interactions may play a critical role in cell physiology but they are not easily detectable in "in vitro" experiments. To detect these weak interactions, we have developed a strategy that included: (a) design of a rapid and very effective crosslinking of protein-protein complexes with poly-functional reagents; (b) selective adsorption of very large proteins on lowly activated ionic exchangers, based on the need of a multipoint physical adsorption to incorporate the proteins into the matrix; (c) purification by selective adsorption of protein-protein complexes formed by strong protein-protein interactions, via selective adsorption of the complexes on lowly activated ionic exchangers via multi-protein physical adsorption and leaving the non-associated proteins in the solution; (d) reinforcement of very weak protein-protein interactions by selective adsorption of the complex on lowly activated ionic exchange supports via a synergetic cooperation of the weak protein-protein interaction plus the interactions of both proteins with the support enabling the almost full shifting of the equilibrium towards the association position; (e) control of the aggregation state of proteins like BSA, formed by weak protein-protein interactions. In this last case, it seems that the interaction of the protein molecules placed on the borders of the aggregate with the groups on the support partially stabilizes the whole aggregate, although, some molecules of the aggregate cannot interact with the support. The size of the aggregates may be defined by controlling the concentration of ionised groups on the support: the less activated the supports are, the bigger the complexes. In this way, solid-phase proteomics could be a very interesting tool to detect weak protein-protein interactions.
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Affiliation(s)
- Manuel Fuentes
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica-CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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45
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Zhang N, Jiang Y, Zou J, Zhuang S, Jin H, Yu Q. Insights into unbinding mechanisms upon two mutations investigated by molecular dynamics study of GSK3β-axin complex: Role of packing hydrophobic residues. Proteins 2007; 67:941-9. [PMID: 17380482 DOI: 10.1002/prot.21359] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Glycogen synthase kinase 3beta (GSK 3beta) is a key component of several cellular processes including Wnt and insulin signalling pathways. The interaction of GSK3beta with scaffolding peptide axin is thought to be responsible for the effective phosphorylation of beta-catenin, the core effector of Wnt signaling, which has been linked with the occurrence of colon cancer and melanoma. It has been demonstrated that the binding of axin to GSK3beta is abolished by the single-point mutation of Val267 to Gly (V267G) in GSK3beta or Leu392 to Pro (L392P) in axin. Molecular dynamics (MD) simulations were performed on wild type (WT), V267G mutant and L392P one to elucidate the two unbinding mechanisms that occur through different pathways. Besides, rough energy and residue-based energy decomposition were calculated by MM_GBSA (molecular mechanical Generalized_Born surface area) approach to illuminate the instability of the two mutants. The MD simulations of the two mutants and WT reveal that the structure of GSK3beta remains unchanged, while axin moves away from the interfacial hydrophobic pockets in both two mutants. Axin exhibits positional shift in V267G mutant, whereas, losing the hydrogen bonds that are indispensable for stabilizing the helix structure of wild type axin, the helix of axin is distorted in L392P mutant. To conclude, both two mutants destroy the hydrophobic interaction that is essential to the stability of GSK3beta-axin complex.
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Affiliation(s)
- Na Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
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46
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Pinkner JS, Remaut H, Buelens F, Miller E, Åberg V, Pemberton N, Hedenström M, Larsson A, Seed P, Waksman G, Hultgren SJ, Almqvist F. Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria. Proc Natl Acad Sci U S A 2006; 103:17897-902. [PMID: 17098869 PMCID: PMC1693844 DOI: 10.1073/pnas.0606795103] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A chemical synthesis platform with broad applications and flexibility was rationally designed to inhibit biogenesis of adhesive pili assembled by the chaperone-usher pathway in Gram-negative pathogens. The activity of a family of bicyclic 2-pyridones, termed pilicides, was evaluated in two different pilus biogenesis systems in uropathogenic Escherichia coli. Hemagglutination mediated by either type 1 or P pili, adherence to bladder cells, and biofilm formation mediated by type 1 pili were all reduced by approximately 90% in laboratory and clinical E. coli strains. The structure of the pilicide bound to the P pilus chaperone PapD revealed that the pilicide bound to the surface of the chaperone known to interact with the usher, the outer-membrane assembly platform where pili are assembled. Point mutations in the pilicide-binding site dramatically reduced pilus formation but did not block the ability of PapD to bind subunits and mediate their folding. Surface plasmon resonance experiments confirmed that the pilicide interfered with the binding of chaperone-subunit complexes to the usher. These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors.
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Affiliation(s)
- Jerome S. Pinkner
- *Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Han Remaut
- Institute of Structural Molecular Biology, University College London/Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| | - Floris Buelens
- Institute of Structural Molecular Biology, University College London/Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| | - Eric Miller
- *Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Veronica Åberg
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden; and
| | - Nils Pemberton
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden; and
| | - Mattias Hedenström
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden; and
| | - Andreas Larsson
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden; and
| | - Patrick Seed
- *Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Gabriel Waksman
- Institute of Structural Molecular Biology, University College London/Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
- To whom correspondence may be addressed. E-mail:
, , or
| | - Scott J. Hultgren
- *Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- To whom correspondence may be addressed. E-mail:
, , or
| | - Fredrik Almqvist
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden; and
- To whom correspondence may be addressed. E-mail:
, , or
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47
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Yin H, Hamilton AD. Strategies for targeting protein-protein interactions with synthetic agents. Angew Chem Int Ed Engl 2006; 44:4130-63. [PMID: 15954154 DOI: 10.1002/anie.200461786] [Citation(s) in RCA: 375] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of small-molecule modulators of protein-protein interactions is a formidable goal, albeit one that possesses significant potential for the discovery of novel therapeutics. Despite the daunting challenges, a variety of examples exists for the inhibition of two large protein partners with low-molecular-weight ligands. This review discusses the strategies for targeting protein-protein interactions and the state of the art in the rational design of molecules that mimic the structures and functions of their natural targets.
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Affiliation(s)
- Hang Yin
- Yale University, New Haven, CT, USA
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48
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Platis D, Sotriffer CA, Clonis Y, Labrou NE. Lock-and-key motif as a concept for designing affinity adsorbents for protein purification. J Chromatogr A 2006; 1128:138-51. [PMID: 16860333 DOI: 10.1016/j.chroma.2006.06.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 06/16/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
The lock-and-key (LAK) motif, a common structural moiety found in subunit interfaces of glutathione S-transferases (GSTs), plays an important role in biomolecular recognition and quaternary structure integrity. Inspection of the key structural features of the LAK motif prompted the de novo design and combinatorial synthesis of a 13-membered solid-phase ligand library, employing as a lead ligand the Phe-Trz-X structure, mimicking the LAK motif. 1,3,5-Triazine (Trz) was used as the scaffold for assembly, substituted with different LAK-mimetic amino acids. De novo ligand design was effected using bioinformatics and molecular modeling and based on mimicking the interactions of the LAK motif. The library of affinity adsorbents was assessed for binding corn and human serum proteomes and purified proteins of different structure and ligand binding specificity. The results showed remarkable differences in the binding specificity of LAK-mimetic adsorbents for a wide range of proteins, as a consequence of minor changes in ligand structure. One LAK-mimetic adsorbent was integrated in a single-step purification protocol for human monoclonal anti-human immunodeficiency virus 2F5 antibody (mAb 2F5) from spiked corn extract, affording high recovery and purity. The results demonstrate that the principle of natural recognition found in the lock-and-key motif, in combination with de novo combinatorial design, may lead to synthetic affinity ligands, useful in downstream processing and proteomic research.
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Affiliation(s)
- Dimitris Platis
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos, 118 55 Athens, Greece
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49
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Zhou H, Wang DA, Baldini L, Ennis E, Jain R, Carie A, Sebti SM, Hamilton AD. Structure-activity studies on a library of potent calix[4]arene-based PDGF antagonists that inhibit PDGF-stimulated PDGFR tyrosine phosphorylation. Org Biomol Chem 2006; 4:2376-86. [PMID: 16763682 DOI: 10.1039/b515483a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platelet-derived growth factor (PDGF) and its receptor PDGFR are required for tumor growth and angiogenesis, so disruption of the PDGF-PDGFR interaction should lead to starvation of tumors and reduction of tumor growth. Potent PDGF antagonists have been discovered through the synthesis of a series of calix[4]arene-based compounds that are designed to bind to the three-loop region of PDGF. The effect of lower-rim alkylation, linker and number of interacting head groups on the calix[4]arene scaffold on PDGF affinity and cellular activity has been investigated.
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Affiliation(s)
- Huchen Zhou
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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50
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Fuentes M, Pessela BCC, Mateo C, Palomo JM, Batalla P, Fernandez-Lafuente R, Guisan JM. Adsorption Behavior of Bovine Serum Albumin on Lowly Activated Anionic Exchangers Suggests a New Strategy for Solid-Phase Proteomics. Biomacromolecules 2006; 7:1357-61. [PMID: 16602761 DOI: 10.1021/bm060002x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diluted solutions of bovine serum albumin (BSA) (e.g., 0.1 mg /mL) do not form detectable protein large aggregates. Using gel-filtration experiments, we determined that a diluted solution of BSA is 97% monomeric BSA and 3% dimeric. The adsorption of this diluted BSA on highly activated anionic exchangers (e,g., having 40 micromol/wet g) keeps this mainly monomeric form. When supports activated with 2 micromol/wet g are used, only dimers become adsorbed to the support, accounting for 100% of the offered BSA. When the diluted BSA solution is offered to very mildly activated anionic exchangers (even only 0.125 micromol/wet g), an unexpected adsorption of most of the BSA on the support was also observed. These very slightly activated supports are only able to adsorb very large proteins or very large protein-protein complexes, larger than BSA dimers. In fact, a rapid cross-linking of the adsorbed BSA with dextran-aldehyde reveals the formation of very large BSA-BSA complexes with molecular mass higher than 500 000 Da, complexes that may be observed for soluble BSA with very high concentrations but are not detectable at 0.1 mg/mL. Moreover, the size of the aggregates strongly depends on the concentration of the ionized groups on the support: the less activated the supports are, the higher the sizes of the complexes. It seems that the interaction of the BSA molecules on the margins of the BSA aggregate with the groups on the support may stabilize the whole protein aggregate, although some components are not interacting with the support. Aggregates could account for more than 40% of the BSA in the solution after 50 h of incubation. However, only these large BSA aggregates were adsorbed in the support.
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Affiliation(s)
- Manuel Fuentes
- Departamento de Biocatalisis, Instituto de Catalisis, Consejo Superior de Investigaciones Científicas, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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