Binding of HasA by its transmembrane receptor HasR follows a conformational funnel mechanism
| Autor: | Audrey Boniface-Guiraud, Stefanie Becker, Philippe Delepelaire, Simon Becker, Kay Diederichs, Thomas E. Exner, Wolfram Welte |
|---|---|
| Přispěvatelé: | Laboratoire de biologie physico-chimique des protéines membranaires (LBPC-PM (UMR_7099)), Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Fachbereich Biologie, University of Konstanz |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Heme acquisition system business.product_category Mutant Biophysics Receptors Cell Surface Heme Molecular Dynamics Simulation 01 natural sciences 03 medical and health sciences chemistry.chemical_compound Molecular dynamics Bacterial Proteins ddc:570 HasR 0103 physical sciences Receptor ComputingMilieux_MISCELLANEOUS Serratia marcescens Physics Binding Sites 010304 chemical physics HasA Crystal structure Membrane Proteins [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology General Medicine Periplasmic space [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology Transmembrane protein [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biomolecules [q-bio.BM] Outer membrane 030104 developmental biology chemistry Mutation Original Article Funnel Bacterial outer membrane business Carrier Proteins Protein Binding |
| Zdroj: | European Biophysics Journal European Biophysics Journal, Springer Verlag (Germany), 2020, 49 (1), pp.39-57. ⟨10.1007/s00249-019-01411-1⟩ |
| ISSN: | 1432-1017 0175-7571 |
| Popis: | HasR in the outer membrane of Serratia marcescens binds secreted, heme-loaded HasA and translocates the heme to the periplasm to satisfy the cell’s demand for iron. The previously published crystal structure of the wild-type complex showed HasA in a very specific binding arrangement with HasR, apt to relax the grasp on the heme and assure its directed transfer to the HasR-binding site. Here, we present a new crystal structure of the heme-loaded HasA arranged with a mutant of HasR, called double mutant (DM) in the following that seemed to mimic a precursor stage of the abovementioned final arrangement before heme transfer. To test this, we performed first molecular dynamics (MD) simulations starting at the crystal structure of the complex of HasA with the DM mutant and then targeted MD simulations of the entire binding process beginning with heme-loaded HasA in solution. When the simulation starts with the former complex, the two proteins in most simulations do not dissociate. When the mutations are reverted to the wild-type sequence, dissociation and development toward the wild-type complex occur in most simulations. This indicates that the mutations create or enhance a local energy minimum. In the targeted MD simulations, the first protein contacts depend upon the chosen starting position of HasA in solution. Subsequently, heme-loaded HasA slides on the external surface of HasR on paths that converge toward the specific arrangement apt for heme transfer. The targeted simulations end when HasR starts to relax the grasp on the heme, the subsequent events being in a time regime inaccessible to the available computing power. Interestingly, none of the ten independent simulation paths visits exactly the arrangement of HasA with HasR seen in the crystal structure of the mutant. Two factors which do not exclude each other could explain these observations: the double mutation creates a non-physiologic potential energy minimum between the two proteins and /or the target potential in the simulation pushes the system along paths deviating from the low-energy paths of the native binding processes. Our results support the former view, but do not exclude the latter possibility. Electronic supplementary material The online version of this article (10.1007/s00249-019-01411-1) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink