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Interlandi G. Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular dynamics simulations. Proteins 2024; 92:117-133. [PMID: 37700555 PMCID: PMC10873117 DOI: 10.1002/prot.26588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the surface of infected cells. Under normal conditions, the two domains are docked to each other and LD binds mannose weakly. However, in the presence of tensile force generated by shear the domains separate and conformational changes propagate across LD resulting in a stronger bond to mannose. Recently, the crystallographic structure of a variant of FimH has been resolved, calledFimH FocH , where PD contains 10 mutations near the inter-domain interface. Although the X-ray structures of FimH andFimH FocH are almost identical, experimental evidence shows thatFimH FocH is activated even in the absence of shear. Here, molecular dynamics simulations combined with the Jarzynski equality were used to investigate the discrepancy between the crystallographic structures and the functional assays. The results indicate that the free energy barrier of the unbinding process between LD and PD is drastically reduced inFimH FocH . Rupture of inter-domain hydrogen bonds involving R166 constitutes a rate limiting step of the domain separation process and occurs more readily inFimH FocH than FimH. In conclusion, the mutations inFimH FocH shift the equilibrium toward an equal occupancy of bound and unbound states for LD and PD by reducing a rate limiting step.
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Affiliation(s)
- Gianluca Interlandi
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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Leusmann S, Ménová P, Shanin E, Titz A, Rademacher C. Glycomimetics for the inhibition and modulation of lectins. Chem Soc Rev 2023; 52:3663-3740. [PMID: 37232696 PMCID: PMC10243309 DOI: 10.1039/d2cs00954d] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 05/27/2023]
Abstract
Carbohydrates are essential mediators of many processes in health and disease. They regulate self-/non-self- discrimination, are key elements of cellular communication, cancer, infection and inflammation, and determine protein folding, function and life-times. Moreover, they are integral to the cellular envelope for microorganisms and participate in biofilm formation. These diverse functions of carbohydrates are mediated by carbohydrate-binding proteins, lectins, and the more the knowledge about the biology of these proteins is advancing, the more interfering with carbohydrate recognition becomes a viable option for the development of novel therapeutics. In this respect, small molecules mimicking this recognition process become more and more available either as tools for fostering our basic understanding of glycobiology or as therapeutics. In this review, we outline the general design principles of glycomimetic inhibitors (Section 2). This section is then followed by highlighting three approaches to interfere with lectin function, i.e. with carbohydrate-derived glycomimetics (Section 3.1), novel glycomimetic scaffolds (Section 3.2) and allosteric modulators (Section 3.3). We summarize recent advances in design and application of glycomimetics for various classes of lectins of mammalian, viral and bacterial origin. Besides highlighting design principles in general, we showcase defined cases in which glycomimetics have been advanced to clinical trials or marketed. Additionally, emerging applications of glycomimetics for targeted protein degradation and targeted delivery purposes are reviewed in Section 4.
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Affiliation(s)
- Steffen Leusmann
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Petra Ménová
- University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Elena Shanin
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
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Liu J, Amaral LAN, Keten S. A new approach for extracting information from protein dynamics. Proteins 2023; 91:183-195. [PMID: 36094321 PMCID: PMC9844508 DOI: 10.1002/prot.26421] [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: 02/28/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/19/2023]
Abstract
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.
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Affiliation(s)
- Jenny Liu
- Department of Mechanical Engineering, Northwestern University
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University
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Sokurenko EV, Tchesnokova V, Interlandi G, Klevit R, Thomas WE. Neutralizing antibodies against allosteric proteins: insights from a bacterial adhesin. J Mol Biol 2022; 434:167717. [DOI: 10.1016/j.jmb.2022.167717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022]
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Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear. J Mol Biol 2022; 434:167681. [PMID: 35697293 DOI: 10.1016/j.jmb.2022.167681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022]
Abstract
The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an 'inactive' conformation with fast binding to mannose to an 'active' conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. This concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.
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Liu J, Amaral LAN, Keten S. A new approach for extracting information from protein dynamics. ARXIV 2022:arXiv:2203.08387v1. [PMID: 35313540 PMCID: PMC8936122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.
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Affiliation(s)
- Jenny Liu
- Department of Mechanical Engineering, Northwestern University
| | - Luís A N Amaral
- Department of Chemical and Biological Engineering, Northwestern University
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University
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