MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Amyloid-β (Aβ) is present in humans as a 39- to 42-amino acid residue metabolic product of the amyloid precursor protein. Although the two predominant forms, Aβ(1–40) and Aβ(1–42), differ in only two residues, they display different biophysical, biological, and clinical behavior. Aβ(1–42) is the more neurotoxic species, aggregates much faster, and dominates in senile plaque of Alzheimer’s disease (AD) patients. Although small Aβ oligomers are believed to be the neurotoxic species, Aβ amyloid fibrils are, because of their presence in plaques, a pathological hallmark of AD and appear to play an important role in disease progression through cell-to-cell transmissibility. Here, we solved the 3D structure of a disease-relevant Aβ(1–42) fibril polymorph, combining data from solid-state NMR spectroscopy and mass-per-length measurements from EM. The 3D structure is composed of two molecules per fibril layer, with residues 15–42 forming a double-horseshoe–like cross–β-sheet entity with maximally buried hydrophobic side chains. Residues 1–14 are partially ordered and in a β-strand conformation, but do not display unambiguous distance restraints to the remainder of the core structure.

https://www.pnas.org/content/pnas/113/34/E4976.full.pdf

Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.

/pdf/developing-a-molecular-dynamics-force-field-for-both-folded-56qvedr22r.pdf

Developing a molecular dynamics force field for both folded and disordered protein states.

Intracellular aggregation of the human amyloid protein α-synuclein is causally linked to Parkinson’s disease. While the isolated protein is intrinsically disordered, its native structure in mammalian cells is not known. Here we use nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy to derive atomic-resolution insights into the structure and dynamics of α-synuclein in different mammalian cell types. We show that the disordered nature of monomeric α-synuclein is stably preserved in non-neuronal and neuronal cells. Under physiological cell conditions, α-synuclein is amino-terminally acetylated and adopts conformations that are more compact than when in buffer, with residues of the aggregation-prone non-amyloid-β component (NAC) region shielded from exposure to the cytoplasm, which presumably counteracts spontaneous aggregation. These results establish that different types of crowded intracellular environments do not inherently promote α-synuclein oligomerization and, more generally, that intrinsic structural disorder is sustainable in mammalian cells. Atomic resolution in-cell NMR and EPR spectroscopy show that the human amyloid protein α-synuclein remains disordered within all mammalian cells tested, including neurons, and identifies which parts of the protein dynamically interact or remain shielded from the cytoplasm, thus counteracting aggregation under physiological cell conditions. Amyloid aggregates of the protein α-synuclein are associated with Parkinson's disease and although the isolated protein is disordered in vitro, various conformations have been proposed for the protein in its physiological context in vivo, ranging from disordered monomers to folded helical tetramers. Now, using atomic-resolution in-cell NMR and EPR spectroscopy, Philipp Selenko and colleagues show that α-synuclein remains disordered within all mammalian cells tested, including neurons, and identify which parts of the protein dynamically interact with, or remain shielded from the cytoplasm, thus preventing aggregation in physiological conditions. The study presents several experimental methods applied for the first time to a protein inside mammalian cells.

/pdf/structural-disorder-of-monomeric-a-synuclein-persists-in-1qwd5xn4g9.pdf

Structural disorder of monomeric α-synuclein persists in mammalian cells

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins.

http://www.drugdesign.gr/uploads/7/6/0/2/7602318/lindorff-larsen2012-comparisons.pdf

Systematic validation of protein force fields against experimental data.

A general method to enhance the sensitivity of the multidimensional NMR experiments performed at high-polarizing magnetic field via the significant reduction of the longitudinal proton relaxation times is described. The method is based on the use of two vast pools of "thermal bath" 1H spins residing on hydrogens covalently attached to carbon and oxygen atoms in 13C,15N labeled and fully protonated or fractionally deuterated proteins to uniformly enhance longitudinal relaxation of the 1HN spins and concomitantly the sensitivity of multipulse NMR experiments. The proposed longitudinal relaxation optimization is implemented in the 2D [15N,1H]-LTROSY, 2D [15N,1H]-LHSQC and 3D LTROSY-HNCA experiments yielding the factor 2-2.5 increase of the maximal signal-to-noise ratio per unit time at 600 MHz. At 900 MHz, the predicted decrease of the 1HN longitudinal relaxation times can be as large as one order of magnitude, making the proposed method an important tool for protein NMR at high magnetic fields.

Longitudinal 1H Relaxation Optimization in TROSY NMR Spectroscopy

A highly active, monomeric chorismate mutase, obtained by topological redesign of a dimeric helical bundle enzyme from Methanococcus jannaschii, was investigated by NMR and various other biochemical techniques, including H/D exchange. Although structural disorder is generally considered to be incompatible with efficient catalysis, the monomer, unlike its natural counterpart, unexpectedly possesses all of the characteristics of a molten globule. Global conformational ordering, observed upon binding of a transition state analog, indicates that folding can be coupled to catalysis with minimal energetic penalty. These results support the suggestion that many modern enzymes might have evolved from molten globule precursors. Insofar as their structural plasticity confers relaxed substrate specificity and/or catalytic promiscuity, molten globules may also be attractive starting points for the evolution of new catalysts in the laboratory.

https://www.pnas.org/content/pnas/101/35/12860.full.pdf

An enzymatic molten globule: efficient coupling of folding and catalysis.

3JHN,Hα, 3JHN,Cβ, and 3JHN,C‘ couplings, all related to the backbone torsion angle φ, were measured for the third immunoglobulin binding domain of protein G, or GB3. Measurements were carried out u...

Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

The nuclear Overhauser effect from a quantitative perspective.

Although protein dynamics has been recognized as a potentially important contributor to enzyme catalysis, structural disorder is generally considered to reduce catalytic efficiency. This widely held assumption has recently been challenged by the finding that an engineered chorismate mutase combines high catalytic activity with the properties of a molten globule, a loosely packed and highly dynamic conformational ensemble. Taking advantage of the ordering observed upon ligand binding, we have now used NMR spectroscopy to characterize this enzyme in complex with a transition-state analog. The complex adopts a helix-bundle structure, as designed, but retains unprecedented flexibility on the millisecond timescale across its entire length. Moreover, pre-steady-state kinetics data show that binding occurs by an induced-fit mechanism on the same timescale as the enzymatic reaction, linking global conformational plasticity with efficient catalysis.

Beat Vögeli

Papers

Longitudinal 1H Relaxation Optimization in TROSY NMR Spectroscopy

An enzymatic molten globule: efficient coupling of folding and catalysis.

Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

The nuclear Overhauser effect from a quantitative perspective.

Structure and dynamics of a molten globular enzyme.