225 research outputs found
Encounter complexes and dimensionality reduction in protein-protein association
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition
Modern Theory of Creep of Reinforced Concrete
The important features of the theory of creep of reinforced concrete, identified and published earlier, are explored. The creation and development of the theory of creep of reinforced concrete is based on non-scientific principles take from systems of classical mechanics that do not correspond to this theory. A detailed analysis of the theory used in many countries was performed, while five oversimplifications were identified that reject fundamental experiments, Eurocodes, rules of mathematics and mechanics: listed in the law of creep, oversimplifications that grossly distort the calculation results, not only the deformations themselves, but also subsequent methods for calculating reinforced concrete structures. These include: unnecessarily modified classical Hooke’s law; imposing a property missing from concrete - an algebraic measure of creep; erroneous superposition principle; use of viscoelastic deformations instead of instantaneous nonlinear plastic deformations; replacement of obvious - nonlinear and non-stationary properties of concrete with linear ones, distorting the qualitative side of phenomena inherent only in nonlinear systems. These errors are covered by unreasonable safety factors, which undermines the economic component of the problem, and of the enormous volumes of reinforced concrete used throughout the world, the analyzed unscientific theory of its calculation causes enormous economic damage in global construction
Theory of short-term and long-term resistance of structures based on the principle of plastic fracture
The authors analyze the theory used in many countries, containing two independent directions: 1) the theory of stability of rod systems, including flat frames; 2) the theory of calculation of structural elements from various materials. The main feature of these theories is the application of the principle of plastic fracture. The assumption about a plastic hinge, due to the inconsistency with the experimental data, is supplemented by the incorrect application of theories of infinite elastic deformations, as well as of infinite creep deformations, which are incompatible with this hinge. Using the rules of mathematics, the principles of mechanics and the results of reliable experiments, it has been revealed that the analyzed theory contains several theories for different applications that reject each other, including the erroneous ones
Experimental evidence of the ferroelectric phase transition near the point in liquid water
We studied dielectric properties of nano-sized liquid water samples confined
in polymerized silicates MCM-41 characterized by the porous sizes \sim 3-10nm.
We report the direct measurements of the dielectric constant by the dielectric
spectroscopy method at frequencies 25Hz-1MHz and demonstrate clear signatures
of the second-order phase transition of ferroelectric nature at temperatures
next to the \lambda- point in the bulk supercooled water. The presented results
support the previously developed polar liquid phenomenology and hence establish
its applicability to model actual phenomena in liquid water.Comment: 4 pages, single figur
Fast calculation of thermodynamic and structural parameters of solutions using the 3DRISM model and the multi-grid method
In the paper a new method to solve the tree-dimensional reference interaction
site model (3DRISM) integral equations is proposed. The algorithm uses the
multi-grid technique which allows to decrease the computational expanses.
3DRISM calculations for aqueous solutions of four compounds (argon, water,
methane, methanol) on the different grids are performed in order to determine a
dependence of the computational error on the parameters of the grid. It is
shown that calculations on the grid with the step 0.05\Angstr and buffer
8\Angstr give the error of solvation free energy calculations less than 0.3
kcal/mol which is comparable to the accuracy of the experimental measurements.
The performance of the algorithm is tested. It is shown that the proposed
algorithm is in average more than 12 times faster than the standard Picard
direct iteration method.Comment: the information in this preprint is not up to date. Since the first
publication of the preprint (9 Nov 2011) the algorithm was modified which
allowed to achieve better results. For the new algorithm see the JCTC paper:
DOI: 10.1021/ct200815v, http://pubs.acs.org/doi/abs/10.1021/ct200815
Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis
Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins
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
A Novel Dimeric Inhibitor Targeting Beta2GPI in Beta2GPI/Antibody Complexes Implicated in Antiphospholipid Syndrome
Background: b2GPI is a major antigen for autoantibodies associated with antiphospholipid syndrome (APS), an autoimmune disease characterized by thrombosis and recurrent pregnancy loss. Only the dimeric form of b2GPI generated by anti-b2GPI antibodies is pathologically important, in contrast to monomeric b2GPI which is abundant in plasma. Principal Findings: We created a dimeric inhibitor, A1-A1, to selectively target b2GPI in b2GPI/antibody complexes. To make this inhibitor, we isolated the first ligand-binding module from ApoER2 (A1) and connected two A1 modules with a flexible linker. A1-A1 interferes with two pathologically important interactions in APS, the binding of b2GPI/antibody complexes with anionic phospholipids and ApoER2. We compared the efficiency of A1-A1 to monomeric A1 for inhibition of the binding of b2GPI/antibody complexes to anionic phospholipids. We tested the inhibition of b2GPI present in human serum, b2GPI purified from human plasma and the individual domain V of b2GPI. We demonstrated that when b2GPI/antibody complexes are formed, A1-A1 is much more effective than A1 in inhibition of the binding of b2GPI to cardiolipin, regardless of the source of b2GPI. Similarly, A1-A1 strongly inhibits the binding of dimerized domain V of b2GPI to cardiolipin compared to the monomeric A1 inhibitor. In the absence of anti-b2GPI antibodies, both A1-A1 and A1 only weakly inhibit the binding of pathologically inactive monomeric b2GPI to cardiolipin. Conclusions: Our results suggest that the approach of using a dimeric inhibitor to block b2GPI in the pathologica
Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2
International audienceArchaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force field uncertainty, and somewhat lower than the predicted GTP/GDP binding free energy differences. The sign and magnitudes of the differences can thus be interpreted at a semiquantitative level, and are found to be consistent with the experimental binding preferences of ON- and OFF-aIF2
All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers
Alzheimer’s disease (AD) is the most common type
of senile
dementia in aging populations. Amyloid β (Aβ)-mediated
dysregulation of ionic homeostasis is the prevailing underlying mechanism
leading to synaptic degeneration and neuronal death. Aβ-dependent
ionic dysregulation most likely occurs either directly via unregulated
ionic transport through the membrane or indirectly via Aβ binding
to cell membrane receptors and subsequent opening of existing ion
channels or transporters. Receptor binding is expected to involve
a high degree of stereospecificity. Here, we investigated whether
an Aβ peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels
can directly mediate Aβ effects even in the absence of receptor–peptide
interactions. Using complementary approaches of planar lipid bilayer
(PLB) electrophysiological recordings and molecular dynamics (MD)
simulations, we show that the d-Aβ isomer exhibits
ion conductance behavior in the bilayer indistinguishable from that
described earlier for the l-Aβ isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance
similar to the l-Aβ isomer channels, and the d-isomer channel conductance is blocked by Zn2+, a known
blocker of l-Aβ isomer channels. MD simulations further
verify formation of β-barrel-like Aβ channels with d- and l-isomers, illustrating that both d- and l-Aβ barrels can conduct cations. The calculated
values of the single-channel conductance are approximately in the
range of the experimental values. These findings are in agreement
with amyloids forming Ca2+ leaking, unregulated channels
in AD, and suggest that Aβ toxicity is mediated through a receptor-independent,
nonstereoselective mechanism
- …