Brigita Urbanc

Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, Dp, Ep, R, C, N, S, T) in GxG peptides in water, for which complete sets of spectroscopic data are available. Amber ff24EXP-GA captures the spectroscopic data for at least 7 guest residues (G, A, V, F, C, T, Ep) better than CHARMM36m and exhibits more amino acid specificity than both the parent Amber ff14SB and CHARMM36m. Amber ff24EXP-GA reproduces the experimental data on three folded proteins and three longer IDPs well, while outperforming Amber ff14SB on short unfolded peptides.

Alzheimer’s disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1−40 and Aβ1−42, other C-terminally truncated Aβ peptides, including Aβ1−38 and Aβ1−43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aβ1−38, Aβ1−40, Aβ1−42, and Aβ1−43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aβ1−38 and Aβ1−40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aβ1−42 and Aβ1−43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aβ1−42) or octamers and pentadecamers (for Aβ1−43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aβ1−42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure–function paradigm governing oligomers formed by various Aβ isoforms.

Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the culprit for the reported discrepancies, we here examine the conformational dynamics of guest glycine and alanine residues in cationic GxG peptides in water using two polarizable MD force fields, CHARMM Drude and AMOEBA. Our results indicate that while AMOEBA captures the experimental data better than CHARMM Drude, neither of the two polarizable force fields offers an improvement of the Ramachandran distributions of glycine and alanine residues in cationic GGG and GAG peptides, respectively, over CHARMM36m.Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the culprit for the reported discrepancies, we here examine the conformational dynamics of guest glycine and alanine residues in cationic GxG peptides in water using two polarizable MD force fields, CHARMM Drude and AMOEBA. Our results indicate that while AMOEBA captures the experimental data better than CHARMM Drude, neither of the two polarizable force fields offers an improvement of the Ramachandran distributions of glycine and alanine residues in cationic GGG and GAG peptides, respectively, over CHARMM36m.

Molecular dynamics (MD) is a powerful tool for studying intrinsically disordered proteins, however, its reliability depends on the accuracy of the force field. We assess Amber ff19SB, Amber ff14SB, OPLS-AA/M, and CHARMM36m with respect to their capacity to capture intrinsic conformational dynamics of 14 guest residues x (=G, A, L, V, I, F, Y, D-P, E-P, R, C, N, S, T) in GxG peptides in water. The MD-derived Ramachandran distribution of each guest residue is used to calculate 5 J-coupling constants and amide I ' band profiles to facilitate a comparison to spectroscopic data through reduced chi(2) functions. We show that the Gaussian model, optimized to best fit the experimental data, outperforms all MD force fields by an order of magnitude. The weaknesses of the MD force fields are: (i) insufficient variability of the polyproline II (pPII) population among the guest residues; (ii) oversampling of antiparallel at the expense of transitional beta-strand region; (iii) inadequate sampling of turn-forming conformations for ionizable and polar residues; and (iv) insufficient guest residue-specificity of the Ramachandran distributions. Whereas Amber ff19SB performs worse than the other three force fields with respect to chi(2) values, it accounts for residue-specific pPII content better than the other three force fields. Additional testing of residue-specific RSFF1 and Amber ff14SB combined with TIP4P/2005 on six guest residues x (=A, I, F, D-P, R, S) reveals that residue specificity derived from protein coil libraries or an improved water model alone do not result in significantly lower chi(2) values.

Protein self-assembly plays an important role in cellular processes. Whereas molecular dynamics (MD) represents a powerful tool in studying assembly mechanisms, its predictions depend on the accuracy of underlying force fields, which are known to overly promote protein assembly. We here examine villin headpiece domain, HP36, which remains soluble at concentrations amenable to MD studies. The experimental characterization of soluble HP36 at concentrations of 0.05 to 1 mM reveals concentration-independent 90% monomeric and 10% dimeric populations. Extensive all-atom MD simulations at two protein concentrations, 0.9 and 8.5 mM, probe the HP36 dimer population, stability, and kinetics of dimer formation within two MD force fields, Amber ff14SB and CHARMM36m. MD results demonstrate that whereas CHARMM36m captures experimental HP36 monomer populations at the lower concentration, both force fields overly promote HP36 association at the higher concentration. Moreover, contacts stabilizing HP36 dimers are force-field-dependent. CHARMM36m produces consistently higher HP36 monomer populations, lower association rates, and weaker dependence of these quantities on the protein concentration than Amber ff14SB. Nonetheless, the highest monomer populations and dissociation constants are observed when the TIP3P water model in Amber ff14SB is replaced by TIP4P/2005, showcasing the critical role of the water model in addressing the protein solubility problem in MD.

Intrinsically disordered proteins and intrinsically disordered regions are frequently enriched in charged amino acids. Intrinsically disordered regions are regularly involved in important biological processes in which one or more charged residues is the driving force behind a protein-biomolecule interaction. Several lines of experimental and computational evidence suggest that polypeptides and proteins that carry high net charges have a high preference for extended conformations with average end-to-end distances exceeding expectations for self-avoiding random coils. Here, we show that charged arginine residues even in short glycine-capped model peptides (GRRG and GRRRG) significantly affect the conformational propensities of each other when compared with the intrinsic propensities of a mostly unperturbed arginine in the tripeptide GRG. A conformational analysis based on experimentally determined J-coupling constants from heteronuclear NMR spectroscopy and amide I' band profiles from vibrational spectroscopy reveals that nearest-neighbor interactions stabilize extended ,3-strand conformations at the expense of polyproline II and turn conformations. The results from molecular dynamics simulations with a CHARMM36m force field and TI P3P water reproduce our results only to a limited extent. The use of the Ramachandran distribution of the central residue of GRRRG in a calculation of end-to-end distances of polyarginines of different length yielded the expected power law behavior. The scaling coefficient of 0.66 suggests that such peptides would be more extended than predicted by a self-avoiding random walk. Our findings thus support in principle theoretical predictions.

Amyloid beta-protein (A beta) oligomers are broadly viewed as the proximate mediators of toxicity in Alzheimer's disease (AD). Recent studies, however, provide substantial evidence that A beta is involved in protection and repair of the central nervous system whereby A beta oligomer and subsequent fibril formation are integral to its normal antimicrobial and antiviral function. These developments raise a question of what exactly makes A beta oligomers toxic in the context of AD. This Perspective describes a paradigm shift in the search for toxic A beta oligomer species that involves oxidative-stress-induced stabilization of A beta oligomers via cross-linking and reviews most recent research elucidating structural aspects of cross-linked A beta oligomers and potential inhibition of their toxicity.

In vitro, cationic glycylalanylglycine (GAG) forms a hydrogel in binary mixtures of water and ethanol. In water, alanine residue is known for its high polyproline II (pPII) content. Spectroscopic data, including three J-coupling constants and amide I' profiles, indicate that addition of 42% ethanol to water significantly reduces the pPII content of alanine residue in GAG. Here, experiment-based Gaussian Ramachandran distributions of alanine in GAG at different ethanol fractions are examined and three MD force fields are evaluated with respect to their ability to capture these ethanol-induced conformational changes. MD simulations on monomeric GAG in eight different water/ethanol mixtures within Amber ff14SB, OPLS-AA/M, and CHARMM36m reveal that only Amber ff14SB partially captures the ethanol-induced conformational changes of alanine residue in monomeric GAG when 42% ethanol is added to water. MD simulations of 200 mM GAG ensembles in pure water and in the aqueous solution with 42% ethanol showcase the ability of CHARMM36m to capture the effect of ethanol on the average pPII content of alanine in GAG and provide a plausible explanation for this effect, which may stem from an increased propensity of GAG to form oligomers in the presence of ethanol.