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Liu G, Ekmen E, Jalalypour F, Mertens HDT, Jeffries CM, Svergun D, Atilgan AR, Atilgan C, Sayers Z. Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations. J Chem Phys 2023; 158:085101. [PMID: 36859088 DOI: 10.1063/5.0136558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment. While we show that these changes fall within the detectable range for SAXS as evidenced by differences observed in the theoretical scattering patterns calculated from the crystal structure models of apo and holo forms, detection of conformational changes due to the point mutation D52A and changes in ionic strength (IS) from SAXS scattering profiles have been challenging. Here, to reach conclusions, statistical analyses with SAXS profiles and results from different techniques were combined in a complementary fashion. The SAXS data complemented by size exclusion chromatography point to multiple and/or alternative conformations at physiological IS, whereas they are well-explained by single crystallographic structures in low IS buffers. By fitting the SAXS data with unique conformations sampled by a series of MD simulations under conditions mimicking the buffers, we quantify the populations of the occupied substates. We also find that the D52A mutant that we predicted by coarse-grained computational modeling to allosterically control the iron binding site in FbpA, responds to the environmental changes in our experiments with conformational selection scenarios that differ from those of the wild type.
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Affiliation(s)
- Goksin Liu
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Erhan Ekmen
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Farzaneh Jalalypour
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Ali Rana Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Canan Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
| | - Zehra Sayers
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Türkiye
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2
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Fındık BK, Cilesiz U, Bali SK, Atilgan C, Aviyente V, Dedeoglu B. Investigation of iron release from the N- and C-lobes of human serum transferrin by quantum chemical calculations. Org Biomol Chem 2022; 20:8766-8774. [DOI: 10.1039/d2ob01518h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cluster models of iron binding sites of the N- and C-lobes highlights the inequivalence of each lobe in iron release.
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Affiliation(s)
- Basak Koca Fındık
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Umut Cilesiz
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Semiha Kevser Bali
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı-Tuzla, Istanbul, 34956, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Burcu Dedeoglu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey
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Abdizadeh H, Jalalypour F, Atilgan AR, Atilgan C. A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs. Front Mol Biosci 2020; 7:210. [PMID: 33195399 PMCID: PMC7477071 DOI: 10.3389/fmolb.2020.00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 11/13/2022] Open
Abstract
We address the problem of triggering dissociation events between proteins that have formed a complex. We have collected a set of 25 non-redundant, functionally diverse protein complexes having high-resolution three-dimensional structures in both the unbound and bound forms. We unify elastic network models with perturbation response scanning (PRS) methodology as an efficient approach for predicting residues that have the propensity to trigger dissociation of an interacting protein pair, using the three-dimensional structures of the bound and unbound proteins as input. PRS reveals that while for a group of protein pairs, residues involved in the conformational shifts are confined to regions with large motions, there are others where they originate from parts of the protein unaffected structurally by binding. Strikingly, only a few of the complexes have interface residues responsible for dissociation. We find two main modes of response: In one mode, remote control of dissociation in which disruption of the electrostatic potential distribution along protein surfaces play the major role; in the alternative mode, mechanical control of dissociation by remote residues prevail. In the former, dissociation is triggered by changes in the local environment of the protein, e.g., pH or ionic strength, while in the latter, specific perturbations arriving at the controlling residues, e.g., via binding to a third interacting partner is required for decomplexation. We resolve the observations by relying on an electromechanical coupling model which reduces to the usual elastic network result in the limit of the lack of coupling. We validate the approach by illustrating the biological significance of top residues selected by PRS on select cases where we show that the residues whose perturbation leads to the observed conformational changes correspond to either functionally important or highly conserved residues in the complex.
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Affiliation(s)
- Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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Jalalypour F, Sensoy O, Atilgan C. Perturb-Scan-Pull: A Novel Method Facilitating Conformational Transitions in Proteins. J Chem Theory Comput 2020; 16:3825-3841. [PMID: 32324386 DOI: 10.1021/acs.jctc.9b01222] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conformational transitions in proteins facilitate precise physiological functions. Therefore, it is crucial to understand the mechanisms underlying these processes to modulate protein function. Yet, studying structural and dynamical properties of proteins is notoriously challenging due to the complexity of the underlying potential energy surfaces (PES). We have previously developed the perturbation-response scanning (PRS) method to identify key residues that participate in the communication network responsible for specific conformational transitions. PRS is based on a residue-by-residue scan of the protein to determine the subset of residues/forces which provide the closest conformational change leading to a target conformational state, inasmuch as linear response theory applies to these motions. Here, we develop a novel method to further evaluate if conformational transitions may be triggered on the PES. We aim to study functionally relevant conformational transitions in proteins by using results obtained from PRS and feeding them as inputs to steered molecular dynamics simulations. The success and the transferability of the method are evaluated on three protein systems having different complexities of motion on the PES: calmodulin, adenylate kinase, and bacterial ferric binding protein. We find that the method captures the target conformation, while providing key residues and the optimum paths with relatively low free energy profiles.
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Affiliation(s)
- Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Ozge Sensoy
- School of Engineering and Natural Sciences, Istanbul Medipol University, 34810, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center, SUNUM, 34956, Istanbul, Turkey
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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Abdizadeh H, Tamer YT, Acar O, Toprak E, Atilgan AR, Atilgan C. Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Phys Chem Chem Phys 2018; 19:11416-11428. [PMID: 28422217 DOI: 10.1039/c7cp01458a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme with an essential role in cell metabolism. DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is a precursor for purine and thymidylate synthesis. Several DHFR targeting antifolate drugs including trimethoprim, a competitive antibacterial inhibitor, have therefore been developed and are clinically used. Evolution of resistance against antifolates is a common public health problem rendering these drugs ineffective. To combat the resistance problem, it is important to understand resistance-conferring changes in the DHFR structure and accordingly develop alternative strategies. Here, we structurally and dynamically characterize Escherichia coli DHFR in its wild type (WT) and trimethoprim resistant L28R mutant forms in the presence of the substrate and its inhibitor trimethoprim. We use molecular dynamics simulations to determine the conformational space, loop dynamics and hydrogen bond distributions at the active site of DHFR for the WT and the L28R mutant. We also report their experimental kcat, Km, and Ki values, accompanied by isothermal titration calorimetry measurements of DHFR that distinguish enthalpic and entropic contributions to trimethoprim binding. Although mutations that confer resistance to competitive inhibitors typically make enzymes more promiscuous and decrease affinity to both the substrate and the inhibitor, strikingly, we find that the L28R mutant has a unique resistance mechanism. While the binding affinity differences between the WT and the mutant for the inhibitor and the substrate are small, the newly formed extra hydrogen bonds with the aminobenzoyl glutamate tail of DHF in the L28R mutant leads to increased barriers for the dissociation of the substrate and the product. Therefore, the L28R mutant indirectly gains resistance by enjoying prolonged binding times in the enzyme-substrate complex. While this also leads to slower product release and decreases the catalytic rate of the L28R mutant, the overall effect is the maintenance of a sufficient product formation rate. Finally, the experimental and computational analyses together reveal the changes that occur in the energetic landscape of DHFR upon the resistance-conferring L28R mutation. We show that the negative entropy associated with the binding of trimethoprim in WT DHFR is due to water organization at the binding interface. Our study lays the framework to study structural changes in other trimethoprim resistant DHFR mutants.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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Abdizadeh H, Atilgan AR, Atilgan C. Mechanisms by Which Salt Concentration Moderates the Dynamics of Human Serum Transferrin. J Phys Chem B 2017; 121:4778-4789. [DOI: 10.1021/acs.jpcb.7b02380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Haleh Abdizadeh
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
| | - Ali Rana Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
| | - Canan Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
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Sensoy O, Atilgan AR, Atilgan C. FbpA iron storage and release are governed by periplasmic microenvironments. Phys Chem Chem Phys 2017; 19:6064-6075. [DOI: 10.1039/c6cp06961d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abdizadeh H, Atilgan C. Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate. Phys Chem Chem Phys 2016; 18:7916-26. [DOI: 10.1039/c5cp05107j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PRS identifies regions contacting rapidly evolving residues that mechanically manipulate dissociation from the pathogen in the human transferrin–bacterial receptor complex.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
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Abdizadeh H, Atilgan AR, Atilgan C. Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH. J Biol Inorg Chem 2015; 20:705-18. [DOI: 10.1007/s00775-015-1256-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/10/2015] [Indexed: 11/30/2022]
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