10 research outputs found
Driving calmodulin protein towards conformational shift by changing ionization states of select residues
Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
"Clumpiness" Mixing in Complex Networks
Three measures of clumpiness of complex networks are introduced. The measures
quantify how most central nodes of a network are clumped together. The
assortativity coefficient defined in a previous study measures a similar
characteristic, but accounts only for the clumpiness of the central nodes that
are directly connected to each other. The clumpiness coefficient defined in the
present paper also takes into account the cases where central nodes are
separated by a few links. The definition is based on the node degrees and the
distances between pairs of nodes. The clumpiness coefficient together with the
assortativity coefficient can define four classes of network. Numerical
calculations demonstrate that the classification scheme successfully
categorizes 30 real-world networks into the four classes: clumped assortative,
clumped disassortative, loose assortative and loose disassortative networks.
The clumpiness coefficient also differentiates the Erdos-Renyi model from the
Barabasi-Albert model, which the assortativity coefficient could not
differentiate. In addition, the bounds of the clumpiness coefficient as well as
the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure
Protonation States of Remote Residues Affect Binding-Release Dynamics of the Ligand but not the Conformation of apo Ferric Binding Protein
We have studied the apo (Fe3+ free) form of periplasmic ferric binding
protein (FbpA) under different conditions and we have monitored the changes in
the binding and release dynamics of H2PO4- that acts as a synergistic anion in
the presence of Fe3+. Our simulations predict a dissociation constant of
2.20.2 mM which is in remarkable agreement with the experimentally
measured value of 2.30.3 mM under the same ionization strength and pH
conditions. We apply perturbations relevant for changes in environmental
conditions as (i) different values of ionic strength (IS), and (ii) protonation
of a group of residues to mimic a different pH environment. Local perturbations
are also studied by protonation or mutation of a site distal to the binding
region that is known to mechanically manipulate the hinge-like motions of FbpA.
We find that while the average conformation of the protein is intact in all
simulations, the H2PO4- dynamics may be substantially altered by the changing
conditions. In particular, the bound fraction which is 20 for the wild type
system is increased to 50 with a D52A mutation/protonation and further to
over 90 at the protonation conditions mimicking those at pH 5.5. The change
in the dynamics is traced to the altered electrostatic distribution on the
surface of the protein which in turn affects hydrogen bonding patterns at the
active site. The observations are quantified by rigorous free energy
calculations. Our results lend clues as to how the environment versus single
residue perturbations may be utilized for regulation of binding modes in hFbpA
systems in the absence of conformational changes.Comment: 26 pages, 4 figure
Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
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