265 research outputs found
Functional modes of proteins are among the most robust ones
It is shown that a small subset of modes which are likely to be involved in
protein functional motions of large amplitude can be determined by retaining
the most robust normal modes obtained using different protein models. This
result should prove helpful in the context of several applications proposed
recently, like for solving difficult molecular replacement problems or for
fitting atomic structures into low-resolution electron density maps. Moreover,
it may also pave the way for the development of methods allowing to predict
such motions accurately.Comment: 4 pages, 5 figure
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
Experimental investigation of relationship between trauma and bisphosphonate-related osteonecrosis
Background: Bisphosphonate (BP)-related osteonecrosis of the jaw (BRONJ) disease is rare, but there are serious side-effects of BP therapy in patients. In some patients, surgery is needed and could not be cured. Astandard test is not available showing the risk of jaw osteonecrosis in routine use. The measurement of serum C.terminal telopeptide (CTX) levels has been used in diseases of BRONJ resorption and antiresorptive therapy.Aim: This paper is aimed at investigating the relationship betweenΒ traumatic procedures and presence of BP-related osteonecrosis.Materials and Methods: Thirty male Wistar albino rats with weighing 200 } 20 g were used for the experimental procedures. Rats were randomly divided into three groups each containing 10 rats as follows: Group 1 (traumatic extraction group), Group 2 (atraumatic extraction group), and Group 3 (control group). All groups, zoledronic acid (ZA) (0.3Β mg/kg/week)[1] was diluted with physiological saline and givenΒ subcutaneously for 2 months. After the 2 months, Group 1 was subjected totraumatic extraction of right first lower molars, and Group 2 was subjected to atraumatic extractions of the right first lower molars. Group 3 was subjected to no extractions as a control group. Animals were euthanized 32 days after tooth extractions, and the ZA administration protocol was maintained until the animalsf death. After sacrifice, blood samples were collected for C-terminal cross.linking telopeptide of type I collagen (CTX.1) levels, clinical and radiological findings were recorded.Results: The bone resorption marker CTX-1 showed a significant difference among the groups. CTX-1 was measured significantly higher in blood samples of Group 2 (4.15 } 0.34; P = 0.001) than Group 1 (3.77 } 0.34; P = 0.0001). No, statistically significant changes were found between Groups 1 and 2 as for clinical and radiological assessment.Conclusion: This study provides preliminary observations for theΒ development of an animal model of BRONJ. Although clinical andΒ radiological findings were not relevant, serum CTX values are reliable biochemical markers for predicting BRONJ and also atraumatic surgical procedures are important to prevent BRONJ.Key words: Bisphosphonates, bone, osteonecrosis, prevention, serum C-terminal telopeptide leve
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
Nonlinearity of Mechanochemical Motions in Motor Proteins
The assumption of linear response of protein molecules to thermal noise or
structural perturbations, such as ligand binding or detachment, is broadly used
in the studies of protein dynamics. Conformational motions in proteins are
traditionally analyzed in terms of normal modes and experimental data on
thermal fluctuations in such macromolecules is also usually interpreted in
terms of the excitation of normal modes. We have chosen two important protein
motors - myosin V and kinesin KIF1A - and performed numerical investigations of
their conformational relaxation properties within the coarse-grained elastic
network approximation. We have found that the linearity assumption is deficient
for ligand-induced conformational motions and can even be violated for
characteristic thermal fluctuations. The deficiency is particularly pronounced
in KIF1A where the normal mode description fails completely in describing
functional mechanochemical motions. These results indicate that important
assumptions of the theory of protein dynamics may need to be reconsidered.
Neither a single normal mode, nor a superposition of such modes yield an
approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure
Prediction of Optimal Folding Routes of Proteins That Satisfy the Principle of Lowest Entropy Loss: Dynamic Contact Maps and Optimal Control
An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of events during folding. We assume that the native state is available. As the protein folds, it makes different set of contacts at different folding steps. The dynamic contact map is constructed from these contacts. The topology of the dynamic contact map changes during the course of folding and this information is utilized in the dynamic optimization model. The solution is obtained using the optimal control theory. We show that the optimal solution can be cast into the form of a Gaussian Network that governs the optimal folding dynamics. Simulation results on three examples (CI2, Sso7d and Villin) show that folding starts by the formation of local clusters. Non-local clusters generally require the formation of several local clusters. Non-local clusters form cooperatively and not sequentially. We also observe that the optimal controller prefers βzippingβ or small loop closure steps during folding. The folding routes predicted by the proposed method bear strong resemblance to the results in the literature
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors (TFs) triggered by small changes in DNA response element (RE) sequences, can spell selectivity in co-factor recruitment. p53-REs are 20-base pair (bp) DNA segments specifying diverse functions. They may be located near the transcription start sites or thousands of bps away in the genome. Their number has been estimated to be in the thousands, and they all share a common motif. A key question is then how does the p53 protein recognize a particular p53-RE sequence among all the similar ones? Here, representative p53-REs regulating diverse functions including cell cycle arrest, DNA repair, and apoptosis were simulated in explicit solvent. Among the major interactions between p53 and its REs involving Lys120, Arg280 and Arg248, the bps interacting with Lys120 vary while the interacting partners of other residues are less so. We observe that each p53-RE quarter site sequence has a unique pattern of interactions with p53 Lys120. The allosteric, DNA sequence-induced conformational and dynamic changes of the altered Lys120 interactions are amplified by the perturbation of other p53-DNA interactions. The combined subtle RE sequence-specific allosteric effects propagate in the p53 and in the DNA. The resulting amplified allosteric effects far away are reflected in changes in the overall p53 organization and in the p53 surface topology and residue fluctuations which play key roles in selective co-factor recruitment. As such, these observations suggest how similar p53-RE sequences can spell the preferred co-factor binding, which is the key to the selective gene transactivation and consequently different functional effects
Static and dynamic characteristics of protein contact networks
The principles underlying protein folding remains one of Nature's puzzles
with important practical consequences for Life. An approach that has gathered
momentum since the late 1990's, looks at protein hetero-polymers and their
folding process through the lens of complex network analysis. Consequently,
there is now a body of empirical studies describing topological characteristics
of protein macro-molecules through their contact networks and linking these
topological characteristics to protein folding. The present paper is primarily
a review of this rich area. But it delves deeper into certain aspects by
emphasizing short-range and long-range links, and suggests unconventional
places where "power-laws" may be lurking within protein contact networks.
Further, it considers the dynamical view of protein contact networks. This
closer scrutiny of protein contact networks raises new questions for further
research, and identifies new regularities which may be useful to parameterize a
network approach to protein folding. Preliminary experiments with such a model
confirm that the regularities we identified cannot be easily reproduced through
random effects. Indeed, the grand challenge of protein folding is to elucidate
the process(es) which not only generates the specific and diverse linkage
patterns of protein contact networks, but also reproduces the dynamic behavior
of proteins as they fold. Keywords: network analysis, protein contact networks,
protein foldingComment: Added Appendix
The Use of Experimental Structures to Model Protein Dynamics
The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very highβfor example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methodsβPrincipal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them
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