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Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations. Int J Mol Sci 2019; 20:ijms20051076. [PMID: 30832287 PMCID: PMC6429128 DOI: 10.3390/ijms20051076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022] Open
Abstract
The combination of hydrodynamic and electrophoretic experiments and computer simulations is a powerful approach to study the interaction between proteins. In this work, we present hydrodynamic and electrophoretic experiments in an aqueous solution along with molecular dynamics and hydrodynamic modeling to monitor and compute biophysical properties of the interactions between the extracellular domain of the HER2 protein (eHER2) and the monoclonal antibody trastuzumab (TZM). The importance of this system relies on the fact that the overexpression of HER2 protein is related with the poor prognosis breast cancers (HER2++ positives), while the TZM is a monoclonal antibody for the treatment of this cancer. We have found and characterized two different complexes between the TZM and eHER2 proteins (1:1 and 1:2 TZM:eHER2 complexes). The conformational features of these complexes regulate their hydrodynamic and electrostatic properties. Thus, the results indicate a high degree of molecular flexibility in the systems that ultimately leads to higher values of the intrinsic viscosity, as well as lower values of diffusion coefficient than those expected for simple globular proteins. A highly asymmetric charge distribution is detected for the monovalent complex (1:1 complex), which has strong implications in correlations between the experimental electrophoretic mobility and the modeled net charge. In order to understand the dynamics of these systems and the role of the specific domains involved, it is essential to find biophysical correlations between dynamics, macroscopic transport and electrostatic properties. The results should be of general interest for researchers working in this area.
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Muneeswaran G, Pandiaraj M, Kartheeswaran S, Sankaralingam M, Muthukumar K, Karunakaran C. Molecular dynamics simulation approach to explore atomistic molecular mechanism of peroxidase activity of apoptotic cytochrome c mutants. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Vega JF, Ramos J, Cruz VL, Vicente-Alique E, Sánchez-Sánchez E, Sánchez-Fernández A, Wang Y, Hu P, Cortés J, Martínez-Salazar J. Molecular and hydrodynamic properties of human epidermal growth factor receptor HER2 extracellular domain and its homodimer: Experiments and multi-scale simulations. Biochim Biophys Acta Gen Subj 2017. [PMID: 28642126 DOI: 10.1016/j.bbagen.2017.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND In a broad range of human carcinomas gene amplification leads to HER2 overexpression, which has been proposed to cause spontaneous dimerization and activation in the absence of ligand. This makes HER2 attractive as a therapeutic target. However, the HER2 homodimerization mechanism remains unexplored. It has been suggested that the "back-to-back" homodimer does not form in solution. Notwithstanding, very recently the crystal structure of the HER2 extracellular domain homodimer formed with a "back-to-head" interaction has been resolved. We intend to explore the existence of such interactions. METHODS A combination of experiments, molecular dynamics and hydrodynamic modeling were used to monitor the transport properties of HER2 in solution. RESULTS & CONCLUSIONS We have detected the HER2 extracellular domain homodimer in solution. The results show a high degree of molecular flexibility, which ultimately leads to quite higher values of the intrinsic viscosity and lower values of diffusion coefficient than those corresponding to globular proteins. This flexibility obeys to the open conformation of the receptor and to the large fluctuations of the different domains. We also report that for obtaining the correct hydrodynamic constants from the modeling one must consider the glycosylation of the systems. GENERAL SIGNIFICANCE Conformational features of epidermal growth factor receptors regulate their hydrodynamic properties and control their activity. It is essential to understand the dynamics of these systems and the role of the specific domains involved. To find biophysical correlations between dynamics and macroscopic transport properties is of general interest for researches working in this area. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- J F Vega
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain.
| | - J Ramos
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
| | - V L Cruz
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
| | - E Vicente-Alique
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
| | - E Sánchez-Sánchez
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
| | - A Sánchez-Fernández
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
| | - Y Wang
- Sino Biological, Inc., Beijing, People's Republic of China
| | - P Hu
- Sino Biological, Inc., Beijing, People's Republic of China
| | - J Cortés
- Ramon y Cajal University Hospital, Ctra. de Colmenar Viejo, km 9,100, 28034 Madrid, Spain; Vall D'Hebron Institute of Oncology (VHIO), Paseo Vall Hebron 119-129, 08035 Barcelona, Spain
| | - J Martínez-Salazar
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, 28006 Madrid, Spain
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Calvanese L, Falcigno L, D'Auria G. Essential dynamics analysis captures the concerted motion of the integrin-binding site in jerdostatin, an RTS disintegrin. Biopolymers 2016; 103:158-66. [PMID: 25363370 DOI: 10.1002/bip.22578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022]
Abstract
Disintegrins, small molecular weight proteins contained in the venom of vipers and rattlesnakes, are high-affinity and selectivity integrin antagonists. Disintegrins inhibitory epitope mainly consists in a tripeptide sequence localized in a mobile loop protruding from the protein core. RTS and/or KTS tripeptide characterizes the most recently discovered group of disintegrins that selectively block α1β1 integrin receptor. A NMR study dedicated to structure and dynamics properties of jerdostatin, an RTS disintegrin, demonstrated that the substitution of the native RTS with KTS motif impaired flexibility and inhibitory activity of the molecule. Here we add atomic details to the experimental profiles of jerdostatin and its R24K mutant by analyzing the dynamics behavior of the molecules through computational methods. For jerdostatin wild type, molecular dynamics simulations and essential dynamics analyses showed that Y31 residue acts as hinge element in the concerted motions involving the active loop and the C-terminal tail. R24 side chain ability to engage both cation-π and H-bond interactions with Y31 residue was found crucial for that breathing mechanism. Less significant loop-tail concerted motions were observed for the R24K mutant. The description at atomic resolution of jerdostatin dynamics is useful for decoding the influence of specific residues on disintegrin functional properties.
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McCabe Pryor M, Steinkamp MP, Halasz AM, Chen Y, Yang S, Smith MS, Zahoransky-Kohalmi G, Swift M, Xu XP, Hanein D, Volkmann N, Lidke DS, Edwards JS, Wilson BS. Orchestration of ErbB3 signaling through heterointeractions and homointeractions. Mol Biol Cell 2015; 26:4109-23. [PMID: 26378253 PMCID: PMC4710241 DOI: 10.1091/mbc.e14-06-1114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
Members of the ErbB family of receptor tyrosine kinases are capable of both homointeractions and heterointeractions. Because each receptor has a unique set of binding sites for downstream signaling partners and differential catalytic activity, subtle shifts in their combinatorial interplay may have a large effect on signaling outcomes. The overexpression and mutation of ErbB family members are common in numerous human cancers and shift the balance of activation within the signaling network. Here we report the development of a spatial stochastic model that addresses the dynamics of ErbB3 homodimerization and heterodimerization with ErbB2. The model is based on experimental measures for diffusion, dimer off-rates, kinase activity, and dephosphorylation. We also report computational analysis of ErbB3 mutations, generating the prediction that activating mutations in the intracellular and extracellular domains may be subdivided into classes with distinct underlying mechanisms. We show experimental evidence for an ErbB3 gain-of-function point mutation located in the C-lobe asymmetric dimerization interface, which shows enhanced phosphorylation at low ligand dose associated with increased kinase activity.
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Affiliation(s)
- Meghan McCabe Pryor
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Mara P Steinkamp
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Adam M Halasz
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Ye Chen
- Department of Mathematics, West Virginia University, Morgantown, WV 25606
| | - Shujie Yang
- Department of OB/GYN, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | | | | | - Mark Swift
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Xiao-Ping Xu
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Dorit Hanein
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Niels Volkmann
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
| | - Jeremy S Edwards
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131 Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131 Cancer Center, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131
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