185 research outputs found
Protein structures and optimal folding emerging from a geometrical variational principle
Novel numerical techniques, validated by an analysis of barnase and
chymotrypsin inhibitor, are used to elucidate the paramount role played by the
geometry of the protein backbone in steering the folding to the correct native
state. It is found that, irrespective of the sequence, the native state of a
protein has exceedingly large number of conformations with a given amount of
structural overlap compared to other compact artificial backbones; moreover the
conformational entropies of unrelated proteins of the same length are nearly
equal at any given stage of folding. These results are suggestive of an
extremality principle underlying protein evolution, which, in turn, is shown to
be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure
Conformations of Proteins in Equilibrium
We introduce a simple theoretical approach for an equilibrium study of
proteins with known native state structures. We test our approach with results
on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and
the alpha spectrin SH3 domain and present evidence for a hierarchical onset of
order on lowering the temperature with significant organization at the local
level even at high temperatures. A further application to the folding process
of HIV-1 protease shows that the model can be reliably used to identify key
folding sites that are responsible for the development of drug resistance .Comment: 6 pages, 3 eps figure
Accuracy of SUPREX (stability of unpurified proteins from rates of H/D exchange) and MALDI mass spectrometry-derived protein unfolding free energies determined under non-EX2 exchange conditions
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
Discrete Kinetic Models from Funneled Energy Landscape Simulations
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an “inside-out”, nucleation-propagation like character
The Free Energy Landscape of Small Molecule Unbinding
The spontaneous dissociation of six small ligands from the active site of FKBP
(the FK506 binding protein) is investigated by explicit water molecular dynamics
simulations and network analysis. The ligands have between four
(dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms,
and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the
FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each
ligand) are grouped according to a set of intermolecular distances into nodes of
a network, and the direct transitions between them are the links. The network
analysis reveals that the bound state consists of several subbasins, i.e.,
binding modes characterized by distinct intermolecular hydrogen bonds and
hydrophobic contacts. The dissociation kinetics show a simple (i.e.,
single-exponential) time dependence because the unbinding barrier is much higher
than the barriers between subbasins in the bound state. The unbinding transition
state is made up of heterogeneous positions and orientations of the ligand in
the FKBP active site, which correspond to multiple pathways of dissociation. For
the six small ligands of FKBP, the weaker the binding affinity the closer to the
bound state (along the intermolecular distance) are the transition state
structures, which is a new manifestation of Hammond behavior. Experimental
approaches to the study of fragment binding to proteins have limitations in
temporal and spatial resolution. Our network analysis of the unbinding
simulations of small inhibitors from an enzyme paints a clear picture of the
free energy landscape (both thermodynamics and kinetics) of ligand
unbinding
Plasmodium falciparum Hep1 is required to prevent the self aggregation of PfHsp70-3
The majority of mitochondrial proteins are encoded in the nucleus and need to be imported from the cytosol into the mitochondria, and molecular chaperones play a key role in the efficient translocation and proper folding of these proteins in the matrix. One such molecular chaperone is the eukaryotic mitochondrial heat shock protein 70 (Hsp70); however, it is prone to self-aggregation and requires the presence of an essential zinc-finger protein, Hsp70-escort protein 1 (Hep1), to maintain its structure and function. PfHsp70-3, the only Hsp70 predicted to localize in the mitochondria of P. falciparum, may also rely on a Hep1 orthologue to prevent self-aggregation. In this study, we identified a putative Hep1 orthologue in P. falciparum and co-expression of PfHsp70-3 and PfHep1 enhanced the solubility of PfHsp70-3. PfHep1 suppressed the thermally induced aggregation of PfHsp70-3 but not the aggregation of malate dehydrogenase or citrate synthase, thus showing specificity for PfHsp70-3. Zinc ions were indeed essential for maintaining the function of PfHep1, as EDTA chelation abrogated its abilities to suppress the aggregation of PfHsp70-3. Soluble and functional PfHsp70-3, acquired by co-expression with PfHep-1, will facilitate the biochemical characterisation of this particular Hsp70 protein and its evaluation as a drug target for the treatment of malaria
Cooperative Transition between Open and Closed Conformations in Potassium Channels
Potassium (K+) ion channels switch between open and closed conformations. The nature of this important transition was revealed by comparing the X-ray crystal structures of the MthK channel from Methanobacterium thermoautotrophicum, obtained in its open conformation, and the KcsA channel from Streptomyces lividans, obtained in its closed conformation. We analyzed the dynamic characteristics and energetics of these homotetrameric structures in order to study the role of the intersubunit cooperativity in this transition. For this, elastic models and in silico alanine-scanning mutagenesis were used, respectively. Reassuringly, the calculations manifested motion from the open (closed) towards the closed (open) conformation. The calculations also revealed a network of dynamically and energetically coupled residues. Interestingly, the network suggests coupling between the selectivity filter and the gate, which are located at the two ends of the channel pore. Coupling between these two regions was not observed in calculations that were conducted with the monomer, which emphasizes the importance of the intersubunit interactions within the tetrameric structure for the cooperative gating behavior of the channel
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