Prediction of Native-State Hydrogen Exchange from Perfectly Funneled Energy Landscapes

Craig, Patricio O.; Lätzer, Joachim; Weinkam, Patrick; Hoffman, Ryan M. B.; Ferreiro, Diego U.; Komives, Elizabeth A.; Wolynes, Peter G.

doi:10.1021/ja207506z

Cited by 70 publications

(124 citation statements)

References 58 publications

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“…First, the MD trajectory used here is based on a realistic physical model with explicit water and stateof-the-art force field (47). An earlier study (45) with similar objectives used a coarse-grained implicit-solvent model and defined the O state as having no C β atom within 6.5 Å of the reference C β atom. This O-state definition is much more disruptive than ours (Fig.…”

Section: Discussionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 99%

“…To date, this approach has been tried only with coarse-grained and/or empirical protein models without explicit solvent (43)(44)(45), or for HX from the denatured-state ensemble (46). The recent availability of ultralong MD simulations with realistic force fields opens up new opportunities in the search for the elusive O state.…”

Section: Significancementioning

confidence: 99%

How amide hydrogens exchange in native proteins

Persson

Halle

2015

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

127

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“…This assumption is also the basis for using G o-type models (9), where only residue-residue contacts present in the native state are energetically favorable by design, leading to a perfect correlation of energy and nativeness (10). These models have successfully predicted a wide range of properties (11), including experimental ϕ-values probing the protein folding mechanism (12), hydrogen exchange protection factors (13), the mechanism of protein-protein association (14,15), domain swapping (16), and misfolding in multidomain proteins (17), to list a few. The same assumption underlies the use of even further simplified Ising-like theoretical models for protein folding based on the native structure (18)(19)(20) and motivates the use of low-dimensional models to interpret folding experiments (21) and simulations (22).…”

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confidence: 99%

Native contacts determine protein folding mechanisms in atomistic simulations

Best

Hummer

Eaton

2013

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

535

562

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The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein α 3 D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms.funnel | internal friction | frustration | reaction coordinate | G o models P rotein folding theory and simulations of coarse-grained models have yielded many insights into the principles that allow a protein to fold rapidly to its native state (1-7). To a great extent, such models have also been successful in reproducing and helping to interpret experimental data. Nonetheless, to be amenable to analytical solution, or to simulations of limited computational complexity, they required certain simplifying assumptions. One of the most powerful assumptions is that only native contacts play a significant role in determining the folding mechanism; this statement is motivated by the so-called "principle of minimal frustration" (1); that is, the folding energy landscape of proteins has been designed by evolution such that the energy is correlated as far as possible with the nativeness of the structure, with local traps due to misfolding or nonnative interactions being reduced or eliminated [leading to a relatively smooth, "funneled" energy landscape (8)]. This assumption is also the basis for using G o-type models (9), where only residue-residue contacts present in the native state are energetically favorable by design, leading to a perfect correlation of energy and nativeness (10). These models have successfully predicted a wide range of properties (11), including experimental ϕ-values probing the protein folding mechanism (12), hydrogen exchange protection factors (13), the mechanism of protein-protein association (14, 15), domain swapping (16), and misfolding in multidomain proteins (17), to list a few. The same assumption underlies the use of even further simplified Ising-like theoretical models for protein folding based on the native structure (18)(19)(20) and motivates the use of low-dimensional models to interpret folding experiments (21) and simulations (22).This native-centric assumption even underlies the interpretation of experimental folding ϕ-values in terms of nat...

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“…Several numerical approaches have been proposed to model HXMS behavior. [33][34][35][36][37][38] Here we present for the first time an analytical solution to calculate the time-dependent evolution 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 of the deuterium distribution for HXMS of a two-state protein governed by the Linderstrøm-Lang model in Fig. 1, under the assumption that exchange through small local fluctuations or "breathing" is negligible (we will discuss the implications of this assumption below).…”

Section: Acs Paragon Plus Environmentmentioning

confidence: 99%

Mapping Protein Conformational Landscapes under Strongly Native Conditions with Hydrogen Exchange Mass Spectrometry

et al. 2015

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The thermodynamic stability and kinetic barriers separating protein conformations under native conditions are critical for proper protein function and understanding dysfunction in diseases of protein conformation. Traditional methods to probe protein unfolding and folding employ denaturants and highly non-native conditions, which may destabilize intermediate species or cause irreversible aggregation especially at the high protein concentrations typically required. Hydrogen exchange (HX) is ideal for detecting conformational behavior under native conditions without the need for denaturants, but detection by NMR is limited to small highly soluble proteins. Mass spectrometry (MS) can, in principle, greatly extend the applicability of native-state HX to larger proteins and lower concentrations. However, quantitative analysis of HXMS profiles is currently limited by experimental and theoretical challenges. Here we address both limitations, by proposing an approach based on using standards to eliminate the systematic experimental artifacts in HXMS profiles, and developing the theoretical framework to describe HX behavior across all regimes based on the Linderstrøm-Lang formalism. We demonstrate proof of principle by a practical application to native-state HX of a globular protein. The framework and the practical tools developed advance the ability of HXMS to extract thermodynamic and kinetic conformational parameters of proteins under native conditions.

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Prediction of Native-State Hydrogen Exchange from Perfectly Funneled Energy Landscapes

Cited by 70 publications

References 58 publications

How amide hydrogens exchange in native proteins

How amide hydrogens exchange in native proteins

Native contacts determine protein folding mechanisms in atomistic simulations

Mapping Protein Conformational Landscapes under Strongly Native Conditions with Hydrogen Exchange Mass Spectrometry

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