Some hows and whys of protein folding

Why do small proteins have such a wide range of folding times? Hue Sun Chan and colleagues at the University of Toronto make a case, using MD simulations, that a critical factor in folding time is the desolvation barrier (A. Ferguson et al., J. Mol. Biol. 389, 619-636; 2009 – yes, an ‘old’ paper, but one I fear I overlooked at the time; paper here). For simulations of 13 proteins, they find that the folding rates span two orders of magnitude if desolvation barriers are not included, but 4.6 orders with those barriers added, which is closer to the range seen experimentally. Moreover, folding in the presence of these solvation effects becomes more cooperative and more channelled, and at the same time sensitive to the native protein’s topological complexity. In other words, if you want to understand protein folding, you probably need explicit water.

Ionizable groups are in a sense ‘incompatible’ with the hydrophobic interiors of proteins, and destabilize the native state, but are nonetheless sometimes found there. Daniel Isom and colleagues at Johns Hopkins consider why (D. G. Isom et al., PNAS 10.1073/pnas.1004213107 – paper not yet online). They do so via mutagenesis experiments that introduce Glu groups into internal hydrophobic sites in staphylococcal nuclease, and measure their pKa values and the effects on protein stability. The Glu groups are accommodated without any major conformational reorganization, suggesting that the protein interior shields the charges surprisingly well, behaving like a material with high dielectric constant. It’s not clear why, although penetration of water is one possibility. Whatever the reason, the results suggest that proteins have somehow (and for some reason) evolved a substantial stability against the internalization of charged groups (albeit with sufficient intolerance not to incorporate them indiscriminately).

Cryoprotectants such as trehalose are also produced by some organisms as a defence against dehydration rather than freezing. But it’s not clear how this protection works. One popular idea is that the sugar simply replaces water molecules hydrating the polar groups of lipids in membranes, or of proteins, maintaining the biomolecules and their aggregates in a fluid state in the face of dehydration. For membranes, the aim must be to prevent the formation of a gel state during dehydration, since this leads to detrimental leakage upon rehydration. This notion is examined by Roland Faller at UC Davis and colleagues using MD simulations (E. A. Golovina et al., Langmuir 26, 11118-11126; 2010 – paper here). They find that the core tenets of the water-replacement hypothesis – replacement of water with trehalose, avoiding a transition to the membranes’ gel state – are borne out, but that the structure of the membrane is different in the presence of trehalose than when fully hydrated.

The precise nature of (charged) lipid hydration is studied by Tahei Tahara and colleagues at RIKEN’s Advanced Science Institute in Saitama, using vibrational sum-frequency generation (J. A. Mondai et al., JACS 10.1021/ja104327t – paper here). They aimed to resolve a discrepancy between hydrogen-down and hydrogen-up water orientations at the interface reported from earlier experiments and simulations, and find that the former seems to hold for cationic lipids and the latter for anionic ones – which I guess is what one would expect on the most simplistic electrostatic grounds.

Manuel Aguilar and colleagues in Spain and Mexico report on MD simulations of the hydration of the tripeptide Cys-Asn-Ser (C. Soriani-Correa et al., J. Phys. Chem. B 114, 8961-8970 (2010) – paper here). Hydration stabilizes a more extended structure of the tripeptide than in the gas phase, owing to the replacement of intramolecular hydrogen bonds with intermolecular ones to water molecules.

Sorin Lusceac and Michael Vogel at the TU Darmstadt use deuterium NMR to investigate water dynamics in the hydration shell of myoglobin in the region of the 200-220 K dynamical crossover (J. Phys. Chem. B 10.1021/jp103663t – paper here). They observe a gradual change from isotropic to anisotropic rotation as the temperature is lowered from around 230 K. At that temperature the hydration water has access to essentially a continuum of orientational states, while by 165 K it can adopt only a few, maybe two. But this change is gradual: there is no sign of a sharp phase transition around 225 K, which has previously been claimed as the temperature of an abrupt fragile-to-strong transition.

Hydration-water dynamics as a function of protein concentration at ambient temperature are studied by Stephen Meech and coworkers at the University of East Anglia using the ultrafast optical Kerr effect, which can probe picosecond time scales (K. Mazur et al., J. Phys. Chem. B 10.1021/jp106423a – paper here). Below 0.4M peptide concentration (for three dipeptides), the water dynamics are slowed (particularly for hydrophilic peptides) but the water retains a primarily tetrahedral geometry. Above this concentration the dynamics are slower still and the tetrahedral network is perturbed, presumably due to intermolecular H-bonding between the peptides.

In fact, David LeBard and Dmitry Matyushov at Arizona State University argue on the basis of numerical simulations (of three globular proteins) that protein hydration shells have sufficient average orientational ordering among the water molecules to constitute a ferroelectric shell that propagates 3-5 molecular layers into the solvent (J. Phys. Chem. B 114, 9246-9258; 2010 – paper here). They argue that this is consistent with THz dielectric measurements, and say the dynamics are dominated by a slow (nanosecond) component that freezes at the protein’s dynamical transition.

Fluorescent molecules are sometimes used to probe the dynamics of DNA and its hydration sphere. For example, coumarin can be inserted into the double helix in place on an entire base pair, attached to one strand while the other is simply without a base. But as Kristina Furse and Steven Corcelli of the University of Notre Dame point out, this is a non-trivial substitution. So they have used MD to investigate how much this substitution perturbs the native state of DNA and its surrounding water molecules and ions (J. Phys. Chem. B 10/1021/jp105761b – paper here). They find that the effects can be significant – widening of the minor groove, increased flexibility, and increased water mobility. They conclude that this is not a reliable way to study, for example, the highly constrained water in DNA’s minor groove.

Melanin pigments are widely distributed in living organisms – in humans they appear in skin, hair, eyes, brain and liver. Their macromolecular structures are still not fully characterized, but seem to be highly dependent on hydration: water fills the slit-like pore regions between stacked graphitic plates in the pigment aggregates. Maria Grazia Bridelli and Pier Raimondo Crippa at the University of Parma use FTIR spectroscopy to look at this water in melanins under different degrees of hydration (J. Phys. Chem. B 10.1021/jp101833k – paper here). They suggest that the traditional picture of water in melanins being divided into relatively labile and tightly bound fractions is simplistic, and that in fact the distribution of adsorption sites is very heterogeneous, with a large pore size dispersion, and the water environments ranging continuously from highly bound in small pores to more or less bulk-like.

Hua Guo at the University of New Mexico in Albuquerque and coworkers have previously reported a ‘promoted-water’ mechanism, involving an active-site bound water molecule, for the action of carboxypeptidase A (CPA) in proteolysis (D. Xu & H. Guo, JACS 131, 9780; 2009). Now, using quantum MD simulations, they find something similar for the CPA-catalysed cleavage of esters (S. Wu et al., J. Phys. Chem. B 114, 9259-9267; 2010 – paper here). An alternative, ‘anhydrous’ nucleophilic mechanism seems to be ruled out for proteolysis, and the authors say that while it is feasible for esterolysis, it has a considerably higher free-energy barrier than the promoted-water pathway.

Hofmeister effects get subtler the harder you look. The series is reversed, say Pavel Jungwirth and colleagues in Prague and Lund, when ammonium halides are substituted by tetraalkylammonium cations (J. Heyda et al., J. Chem. Phys. B 10.1021/jp101393k – paper here). This effect is predicted by their MD simulations, and confirmed by experiment, and may be rationalized from a consideration of the different hydration structures of the cations.

Dissolved salts seem generally to increase water’s surface tension, and in ways specific to particular anions and cations that mirror the respective Hofmeister effects. Why? Irving Langmuir suggested that there is ion depletion at the interface; now we know that the effects may be subtle, especially at hydrophobic rather than free interfaces. Yan Levin and colleagues in Brazil have a shot at developing a first-principles theory based on an electrostatic approach to calculating Gibbs adsorption isotherms for the ions (A. P. dos Santos et al., Langmuir 26, 10778-10783; 2010 – paper here). They say that ‘kosmotropic’ (I know) anions are depleted at the interface, while chaotropic anions are absorbed (the theory is actually, as far as I can see, silent about the actual hydration structures of the ions). It predicts well the observed trends in surface tensions seen for the corresponding sodium salts.

Amphiphilic proteins tend to segregate to the air-water interface. Berk Hess of the MPI Mainz and colleagues say that the key driving force for small peptides of this type is the dehydration of hydrophobic residues, and that the effect scales linearly with the size of the molecules (O. Engin et al., J. Phys. Chem. B 10.1021/jp1024922 – paper here).

Roumiana Tsenkova at Kobe University and colleagues have proposed that studying water dynamics in biological systems using near-IR spectroscopy can provide a way of monitoring changes in an organism’s biological state – a method they call ‘aquaphotomics’ (see R. Tsenkova, J. Near Infrared Spectrosc. 17,303-313; 2009). They now propose that the technique can identify infection of soybean leaves with soybean mosaic virus in vivo, two weeks before the normal visual signs of infection in the plant (B. Jinendra et al., Biochem. Biophys. Res. Commun. 397, 685-690; 2010 – paper here). Two new NIR bands in the water region turn out to be highly sensitive to infection. The mechanism seems unclear; the authors say only that the virus seems to alter hydration hydrogen-bonded structures in a way that brings the water closer to bulk-like.

Another coarse-grained model for water is presented by Qiang Cui and colleagues at Wisconsin-Madison (Z. Wu et al., J. Phys. Chem. B 10.1021/jp1019763 – paper here). This groups four water molecules into a single site, represented as three electrostatic charges (which approximate the cluster’s dipole and quadrupole moments) and a non-electrostatic ‘soft’ interaction. The model is, however, optimized for the bulk and is considered unlikely to be applicable to ice; one imagines the same might be true of hydration structures in which local cluster geometries are non-bulk-like. A simple, computationally cheap model geared specifically to hydration is offered by Piotr Setny and Martin Zacharias (J. Phys. Chem. B 10.1021/jp102462s – paper here), in which solute-solvent and solvent-solvent interaction energies are calculated in a mean-field approximation on a BCC grid. The model performs well for predicting hydration energies of some drug molecules and for reproducing buried-water distributions in proteins.

I recently came across a nice review article by Felix Sedlmeier, Roland Netz and colleagues at TU Munich on ‘water at polar and nonpolar solid walls (F. Sedlmeier et al., Biointerphases 3(3), FC23-FC39 (2008) – paper here), which looks at what MD simulations have to tell us about statics, dynamics, rheology and so forth. And on this topic, Shu Nie and coworkers at Sandia Labs describe, on the basis of scanning tunnelling microscopy studies, an intriguing interfacial structure for a wetting water layer on Pt(111), in which the ice-like bilayer commonly reported is modified due to the appearance of 5-and 7-membered rings in the first wetting layer (S. Nie et al., Phys. Rev. Lett. 105, 026102; 2010 – paper here).