311 research outputs found
Depth dependent dynamics in the hydration shell of a protein
We study the dynamics of hydration water/protein association in folded
proteins, using lysozyme and myoglobin as examples. Extensive molecular
dynamics simulations are performed to identify underlying mechanisms of the
dynamical transition that corresponds to the onset of amplified atomic
fluctuations in proteins. The number of water molecules within a cutoff
distance of each residue scales linearly with protein depth index and is not
affected by the local dynamics of the backbone. Keeping track of the water
molecules within the cutoff sphere, we observe an effective residence time,
scaling inversely with depth index at physiological temperatures while the
diffusive escape is highly reduced below the transition. A depth independent
orientational memory loss is obtained for the average dipole vector of the
water molecules within the sphere when the protein is functional. While below
the transition temperature, the solvent is in a glassy state, acting as a solid
crust around the protein, inhibiting any large scale conformational
fluctuations. At the transition, most of the hydration shell unfreezes and
water molecules collectively make the protein more flexible.Comment: Journal of Chemical Physics in pres
Some observations on the behavior of the Langley model rotor blade
The design of the model rotor and the comparative study of coupled beam theory and the finite element analysis performed earlier at the Aerostructures Directorate by Robert Hodges and Mark Nixon is examined. Attention is focused upon two matters: (1) an examination of the small discrepancies between twist angle predictions under pure torque and radial loading, and (2) an assessment of nonclassical effects in bending behavior. The primary objective is understanding, particularly with regard to cause and effect relationships. Understanding, together with the simple, affordable nature of the coupled beam analysis, provides a sound basis for design
Anharmonicity and self-similarity of the free energy landscape of protein G
The near-native free energy landscape of protein G is investigated through
0.4 microseconds-long atomistic molecular dynamics simulations in explicit
solvent. A theoretical and computational framework is used to assess the
time-dependence of salient thermodynamical features. While the quasi-harmonic
character of the free energy is found to degrade in a few ns, the slow modes
display a very mild dependence on the trajectory duration. This property
originates from a striking self-similarity of the free energy landscape
embodied by the consistency of the principal directions of the local minima,
where the system dwells for several ns, and of the virtual jumps connecting
them.Comment: revtex, 6 pages, 5 figure
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
Modular logic gates: cascading independent logic gates via metal ion signals
Cataloged from PDF version of article.Abstract
Systematic cascading of molecular logic gates is an important issue to be addressed for advancing research in this field. We have demonstrated that photochemically triggered metal ion signals can be utilized towards that goal. Thus, independent logic gates were shown to work together while keeping their identity in more complex logic designs. Communication through the intermediacy of ion signals is clearly inspired from biological processes modulated by such signals, and implemented here with ion responsive molecules. © 2014 The Royal Society of Chemistry.
Classical, semiclassical, and quantum investigations of the 4-sphere scattering system
A genuinely three-dimensional system, viz. the hyperbolic 4-sphere scattering
system, is investigated with classical, semiclassical, and quantum mechanical
methods at various center-to-center separations of the spheres. The efficiency
and scaling properties of the computations are discussed by comparisons to the
two-dimensional 3-disk system. While in systems with few degrees of freedom
modern quantum calculations are, in general, numerically more efficient than
semiclassical methods, this situation can be reversed with increasing dimension
of the problem. For the 4-sphere system with large separations between the
spheres, we demonstrate the superiority of semiclassical versus quantum
calculations, i.e., semiclassical resonances can easily be obtained even in
energy regions which are unattainable with the currently available quantum
techniques. The 4-sphere system with touching spheres is a challenging problem
for both quantum and semiclassical techniques. Here, semiclassical resonances
are obtained via harmonic inversion of a cross-correlated periodic orbit
signal.Comment: 12 pages, 5 figures, submitted to Phys. Rev.
Near-IR-Triggered, Remote-Controlled Release of Metal Ions: A Novel Strategy for Caged Ions
Cataloged from PDF version of article.A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal-ion affinity upon irradiation with low-energy red/near-IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions
A network model to investigate structural and electrical properties of proteins
One of the main trend in to date research and development is the
miniaturization of electronic devices. In this perspective, integrated
nanodevices based on proteins or biomolecules are attracting a major interest.
In fact, it has been shown that proteins like bacteriorhodopsin and azurin,
manifest electrical properties which are promising for the development of
active components in the field of molecular electronics. Here we focus on two
relevant kinds of proteins: The bovine rhodopsin, prototype of GPCR protein,
and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most
qualified treatments of Alzheimer disease. Both these proteins exert their
functioning starting with a conformational change of their native structure.
Our guess is that such a change should be accompanied with a detectable
variation of their electrical properties. To investigate this conjecture, we
present an impedance network model of proteins, able to estimate the different
electrical response associated with the different configurations. The model
resolution of the electrical response is found able to monitor the structure
and the conformational change of the given protein. In this respect, rhodopsin
exhibits a better differential response than AChE. This result gives room to
different interpretations of the degree of conformational change and in
particular supports a recent hypothesis on the existence of a mixed state
already in the native configuration of the protein.Comment: 25 pages, 12 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
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