Systematic Validation of Protein Force Fields against Experimental Data

Lindorff‐Larsen, Kresten; Maragakis, Paul; Piana, Stefano; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

doi:10.1371/journal.pone.0032131

Cited by 629 publications

(787 citation statements)

References 43 publications

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“…As regards the simulation, the main concern is the quality of the empirical force field. However, the force field used in this simulation (47) has fared very well when benchmarked against NMR data related to conformational flexibility of native proteins (55)(56)(57). Moreover, the MD trajectory used here yields excellent agreement with the NMR-determined exchange times of the four internal water molecules in BPTI (58).…”

Section: Resultsmentioning

confidence: 89%

How amide hydrogens exchange in native proteins

Persson

Halle

2015

Proc. Natl. Acad. Sci. U.S.A.

127

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Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.protein dynamics | hydration | proton transfer | MD simulation | BPTI B efore the tightly packed and densely H-bonded structure of globular proteins had been established, Hvidt and Linderstrøm-Lang (1) showed that all backbone amide hydrogens of insulin exchange with water hydrogens, implying that all parts of the polypeptide backbone are, at least transiently, exposed to solvent. In the following 60 y, hydrogen exchange (HX), usually monitored by NMR spectroscopy (2) or mass spectrometry (3), has been widely used to study protein folding and stability (4-10), structure (11, 12), flexibility and dynamics (13-15), and solvent accessibility and binding (16,17), often with single-residue resolution. However, because the exchange mechanism is unclear, HX data from proteins can, at best, be interpreted qualitatively (18)(19)(20)(21)(22)(23)(24)(25).Under most conditions, amide HX is catalyzed by hydroxide ions (26, 27) at a rate that is influenced by inductive and steric effects from adjacent side chains (28). For unstructured peptides, HX is a slow process simply because the hydroxide concentration is low. For example, at 25°C and pH 4, HX occurs on a time scale of minutes. Under similar conditions, amides buried in globular proteins exchange on a wide range of time scales, extending up to centuries. HX can only occur if the amide is exposed to solvent, so conformational fluctuations must be an integral part of the HX mechanism (18).Under sufficiently destabilizing conditions HX occurs from the denatured-state ensemble, but under native conditions few amides exchange by such global unfolding (9, 29-31). For example, in bovine pancreatic trypsin inhibitor (BPTI), 8 amides in the core β-sheet exchange by global unfolding under native conditions (7, 32), whereas the remaining 45 amides require less extensive conforma...

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Section: Resultsmentioning

confidence: 89%

How amide hydrogens exchange in native proteins

Persson

Halle

2015

Proc. Natl. Acad. Sci. U.S.A.

127

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“…This discrepancy should most likely be ascribed to deficiencies in the force field representation of the system, and may be related to the weak temperature dependence of the stability of helical structures (9). This appears to be a general characteristic of the force fields commonly used for protein simulations (19,20), suggesting that some aspects of protein folding, like helix formation, involve many-body effects that may not be fully reproduced by simple pairwise additive force fields. The importance of such effects is likely to be system-and size-dependent and, while it appears to be possible to get good quantitative agreement with experiment in folding simulations of small proteins with current force fields, folding simulations of larger proteins may require the development of improved functional forms beyond currently used functional forms.…”

Section: Resultsmentioning

confidence: 99%

“…Substantial improvements have also been made in the molecular mechanics force fields used in MD simulations (14,(18)(19)(20).…”

mentioning

confidence: 99%

Protein folding kinetics and thermodynamics from atomistic simulation

Piana

Lindorff‐Larsen

Shaw

2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

284

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Advances in simulation techniques and computing hardware have created a substantial overlap between the timescales accessible to atomic-level simulations and those on which the fastest-folding proteins fold. Here we demonstrate, using simulations of four variants of the human villin headpiece, how simulations of spontaneous folding and unfolding can provide direct access to thermodynamic and kinetic quantities such as folding rates, free energies, folding enthalpies, heat capacities, Φ-values, and temperaturejump relaxation profiles. The quantitative comparison of simulation results with various forms of experimental data probing different aspects of the folding process can facilitate robust assessment of the accuracy of the calculations while providing a detailed structural interpretation for the experimental observations. In the example studied here, the analysis of folding rates, Φ-values, and folding pathways provides support for the notion that a norleucine double mutant of villin folds five times faster than the wild-type sequence, but following a slightly different pathway. This work showcases how computer simulation has now developed into a mature tool for the quantitative computational study of protein folding and dynamics that can provide a valuable complement to experimental techniques.Amber ff99SB*-ILDN | enthalpy | heat capacity | pre-exponential factor | transition path time P roteins are synthesized in the cell or in vitro as unstructured polypeptide chains that, in most cases, self-assemble into their functionally active three-dimensional shapes. This process, called protein folding, occurs on a broad range of timescales ranging from microseconds to seconds and higher. From a purely physical-chemical perspective, it should be possible in principle to characterize the folding mechanism of a given protein at atomistic resolution and to reconstruct its free-energy landscape, given only its primary sequence, through molecular dynamics (MD) simulations based on elementary physical principles. This direct approach has been rarely pursued because even the simplest systems representing a protein immersed in water consist of several thousand atoms, and simulating their behavior on the timescales typical of protein folding is computationally extremely demanding. The discovery and design of fast-folding proteins (1) significantly narrowed the timescale gap between simulations and experiments, making such simulations feasible, at least for the fastest-folding proteins.The C-terminal fragment of the villin headpiece [referred to in the remainder of this paper simply as "villin" (2)], one of the fastest-folding protein domains known (3), has proven to be an excellent target for folding simulations with physics-based force fields and an atomistically detailed representation of both the solute and the surrounding solvent (4-7). Until recently, the length of such simulations was limited to a few microseconds-a timescale sufficient to capture, at best, a single folding event (8,9). With this limitation, it has bee...

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“…64,65 We chose the AMBER99sb*-ILDN force field rather than older versions of AMBER, and the OPLS-AA or GROMOS force field, 66 because it provides a better description of the structural and dynamical properties of well-structured proteins and allows folding of diverse proteins into their NMR structures. 64 The parameters for NQTrp, obtained from quantum calculations, were taken from our previous study. 31 Aβ dimer was initially put in the center of a dodecahedron box with periodic boundary conditions.…”

Section: ■ Methodsmentioning

confidence: 99%

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-l-tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

Zhang

et al. 2013

ACS Chem. Neurosci.

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Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12−28 and 17−42, none of these studies were conducted on the fulllength Aβ1−42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1−42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1−42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1−42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1−42 dimer against AD.

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Systematic Validation of Protein Force Fields against Experimental Data

Cited by 629 publications

References 43 publications

How amide hydrogens exchange in native proteins

How amide hydrogens exchange in native proteins

Protein folding kinetics and thermodynamics from atomistic simulation

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-l-tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

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