Abstract
We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity, yet releases it with ease in the cytoplasm for subsequent use. The observations fit the “conformational selection” model whereby the existence of a weakly populated, higher energy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized. The approach relies on the systematic use of computational perturbation/response techniques based on linear response theory, by sequentially applying directed forces on single-residues along the chain and recording the resulting relative changes in the residue coordinates. We further obtain closed-form expressions for the magnitude and the directionality of the response. Using PRS, we study the ligand release mechanisms of FBP and support the findings by molecular dynamics simulations. We find that the residue-by-residue displacements between the apo and the holo forms, as determined from the X-ray structures, are faithfully reproduced by perturbations applied on the majority of the residues of the apo form. However, once the stabilizing ligand (Fe) is integrated to the system in holo FBP, perturbing only a few select residues successfully reproduces the experimental displacements. Thus, iron uptake by FBP is a favored process in the fluctuating environment of the protein, whereas iron release is controlled by mechanisms including chelation and allostery. The directional analysis that we implement in the PRS methodology implicates the latter mechanism by leading to a few distant, charged, and exposed loop residues. Upon perturbing these, irrespective of the direction of the operating forces, we find that the cap residues involved in iron release are made to operate coherently, facilitating release of the ion.
Highlights
Functional proteins are complex structures, which may remain mainly unmodified as a result of a multitude of mutations [1], yet may have their energy surface go through significant changes upon perturbing highly specific regions [2,3,4]
We develop a toolkit that we term perturbation-response scanning (PRS) which is based on sequential application of Linear response theory (LRT) to study the origins of structural changes undergone by protein molecules
Since ferric binding protein exhibits a high sequence identity with human transferrin whose allosteric anion binding sites generate large conformational changes around the binding region, we suggest mutational studies on remotely controlling sites identified in this work
Summary
Functional proteins are complex structures, which may remain mainly unmodified as a result of a multitude of mutations [1], yet may have their energy surface go through significant changes upon perturbing highly specific regions [2,3,4]. The various accessible states populated may be manipulated by inducing short and longrange conformational changes in the structure [5]; alternatively, a dynamical control may take place without any significant structural variation [6,7]. To explore the presence or the absence of such ‘‘shifts in the energy landscapes,’’ [8] one needs to perturb the protein structure, and observe the response [9]. The response may be measured directly, as a change in the overall conformation of the protein [13], or indirectly, e.g., through determining the kinetic parameters, and proposing kinetic models that explain the observations.[14,15] The purpose in such work is to understand and control the response of the protein for a plethora of reasons, including, but not limited to, the design of efficient drugs [16,17], or to tailor enzymes serving as ‘‘materials.’’[18]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
