580 research outputs found
Compact phases of polymers with hydrogen bonding
We propose an off-lattice model for a self-avoiding homopolymer chain with
two different competing attractive interactions, mimicking the hydrophobic
effect and the hydrogen bond formation respectively. By means of Monte Carlo
simulations, we are able to trace out the complete phase diagram for different
values of the relative strength of the two competing interactions. For strong
enough hydrogen bonding, the ground state is a helical conformation, whereas
with decreasing hydrogen bonding strength, helices get eventually destabilized
at low temperature in favor of more compact conformations resembling
-sheets appearing in native structures of proteins. For weaker hydrogen
bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR
Structure and Thermodynamics of Polyglutamine Peptides and Amyloid Fibrils via Metadynamics and Molecular Dynamics Simulations
Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This dissertation addresses these gaps in knowledge by shedding light on important steps of the aggregation process. The structural motif of polyQ fibrils is not agreed upon in the field, which is worrying, given that these structures are the endpoint of polyQ aggregation. Here, molecular dynamics (MD) simulations paired with UV resonance Raman (UVRR) experiments show that short polyQ peptides adopt extended antiparallel β-sheet fibrils, contrary to β-hairpin structures oft predicted in the polyQ field. The structure of monomeric polyQ peptides was then studied to gain insight into the beginnings of the aggregation mechanism. Metadynamics MD simulations were used to characterize the conformational energy landscape of polyQ peptides, and this data was compared to experimental UVRR results. We found short polyQ peptides can adopt PPII-rich and collapsed β-strand monomeric structures, which establishes that polyQ can form distinct conformational states as monomers. The effect of increased polyQ repeat length was also tested, and it was found that increased repeat length corresponds to lower energy barriers between monomeric conformational states, which may explain why longer polyQ repeats are quicker to aggregate. Hydrogen bonding strengths of polyQ monomers and fibrils were also investigated with MD and UVRR, showing that polyQ peptides favor intrapeptide hydrogen bonds over those between peptide and water. Overall, the work in this dissertation deepens the understanding of the polyQ aggregation mechanism by determining the structure and thermodynamics of monomeric and fibrillar states, as well as identifying polyQ peptide hydrogen bonding as one of the driving forces in these systems. This knowledge can aid the development of molecular mechanisms to interfere with the formation of toxic polyQ aggregates that trigger the onset of polyQ diseases
Conformations and coherences in structure determination by ultrafast electron diffraction
In this article we consider consequences of spatial coherences and conformations in diffraction of (macro)molecules with different potential energy landscapes. The emphasis is on using this understanding to extract structural and temporal information from diffraction experiments. The theoretical analysis of structural interconversions spans an increased range of complexity, from small hydrocarbons to proteins. For each molecule considered, we construct the potential energy landscape and assess the characteristic conformational states available. For molecules that are quasiharmonic in the vicinity of energy minima, we find that the distinct conformer model is sufficient even at high temperatures. If, however, the energy surface is either locally flat around the minima or the molecule includes many degrees of conformational freedom, a Boltzmann ensemble must be used, in what we define as the pseudoconformer approach, to reproduce the diffraction. For macromolecules with numerous energy minima, the ensemble of hundreds of structures is considered, but we also utilize the concept of the persistence length to provide information on orientational coherence and its use to assess the degree of resonance contribution to diffraction. It is shown that the erosion of the resonant features in diffraction which are characteristic of some quasiperiodic structural motifs can be exploited in experimental studies of conformational interconversions triggered by a laser-induced temperature jump
What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model
The thermodynamics of the small SH3 protein domain is studied by means of a
simplified model where each bead-like amino acid interacts with the others
through a contact potential controlled by a 20x20 random matrix. Good folding
sequences, characterized by a low native energy, display three main
thermodynamical phases, namely a coil-like phase, an unfolded globule and a
folded phase (plus other two phases, namely frozen and random coil, populated
only at extremes temperatures). Interestingly, the unfolded globule has some
regions already structured. Poorly designed sequences, on the other hand,
display a wide transition from the random coil to a frozen state. The
comparison with the analytic theory of heteropolymers is discussed
Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions
In the past years, the folding kinetics of many small single-domain proteins
has been characterized by mutational Phi-value analysis. In this article, a
simple, essentially parameter-free model is introduced which derives folding
routes from native structures by minimizing the entropic loop-closure cost
during folding. The model predicts characteristic folding sequences of
structural elements such as helices and beta-strand pairings. Based on few
simple rules, the kinetic impact of these structural elements is estimated from
the routes and compared to average experimental Phi-values for the helices and
strands of 15 small, well-characterized proteins. The comparison leads on
average to a correlation coefficient of 0.62 for all proteins with polarized
Phi-value distributions, and 0.74 if distributions with negative average
Phi-values are excluded. The diffuse Phi-value distributions of the remaining
proteins are reproduced correctly. The model shows that Phi-value
distributions, averaged over secondary structural elements, can often be traced
back to entropic loop-closure events, but also indicates energetic preferences
in the case of a few proteins governed by parallel folding processes.Comment: 24 pages, 3 figures, 2 tables; to appear in "Proteins: Structure,
Function, and Bioinformatics
Solvated dissipative electro-elastic network model of hydrated proteins
Elastic netwok models coarse grain proteins into a network of residue beads
connected by springs. We add dissipative dynamics to this mechanical system by
applying overdamped Langevin equations of motion to normal-mode vibrations of
the network. In addition, the network is made heterogeneous and softened at the
protein surface by accounting for hydration of the ionized residues. Solvation
changes the network Hessian in two ways. Diagonal solvation terms soften the
spring constants and off-diagonal dipole-dipole terms correlate displacements
of the ionized residues. The model is used to formulate the response functions
of the electrostatic potential and electric field appearing in theories of
redox reactions and spectroscopy. We also formulate the dielectric response of
the protein and find that solvation of the surface ionized residues leads to a
slow relaxation peak in the dielectric loss spectrum, about two orders of
magnitude slower than the main peak of protein relaxation. Finally, the
solvated network is used to formulate the allosteric response of the protein to
ion binding. The global thermodynamics of ion binding is not strongly affected
by the network solvation, but it dramatically enhances conformational changes
in response to placing a charge at the active site of the protein
Protein Folding and Misfolding on Surfaces
Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand how a protein folds rapidly and efficiently to the compact, biologically active structure. The increased knowledge on protein folding has highlighted its strict relation to protein misfolding and aggregation, either process being in close competition with the other, both relying on the same physicochemical basis. The theory has also provided information to better understand the structural and environmental factors affecting protein folding resulting in protein misfolding and aggregation into ordered or disordered polymeric assemblies. Among these, particular importance is given to the effects of surfaces. The latter, in some cases make possible rapid and efficient protein folding but most often recruit proteins/peptides increasing their local concentration thus favouring misfolding and accelerating the rate of nucleation. It is also emerging that surfaces can modify the path of protein misfolding and aggregation generating oligomers and polymers structurally different from those arising in the bulk solution and endowed with different physical properties and cytotoxicities
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