The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo-and polypeptides and, surprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured oligo-and polypeptides. The application of this approach to protein studies is discussed.

The hydrogen exchange behavior of native cytochrome c in low concentrations of de-naturant reveals a sequence of metastable, partially unfolded forms that occupy free energy levels reaching up to the fully unfolded state. The step from one form to another is accomplished by the unfolding of one or more cooperative units of structure. The cooperative units are entire omega loops or mutually stabilizing pairs of whole helices and loops. The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.Under native conditions, a small fraction of any population of protein molecules occupies each possible higher energy, partially unfolded state, including even the fully unfolded state, as described by the Boltzmann distribution. The study of these partially unfolded forms (intermediates) may illuminate the fundamental cooperative nature of protein structure and define the unfolding and refolding pathways of a protein even though the intermediates are normally invisible to measurement. The energy levels and therefore the occupation of these conformationally excited states can be manipulated by denaturants and temperature. Hydrogen exchange experiments can then determine the hydrogens exposed in each higher energy form, their rates of exchange with solvent, and their sensitivity to the perturbant. From this we can infer, respectively, the structure, the free energy, and the surface exposure of each protein form.Results for cytochrome c reveal a small sequence of distinct partially unfolded forms with progressively increasing free energy and degree of unfolding. These appear to represent the major intermediates in the unfolding and refolding pathways of cytochrome c. Hydrogen exchange theoryExchangeable amide hydrogens (NH) that are involved in hydrogen-bonded structure can exchange with solvent hydrogens only when they are transiently exposed to solvent in some kind of closed to open reaction (1-3), as indicated in Eq. 1.(1)In the almost universally observed limiting case, referred to as EX2 (for bimolecular exchange) (1), the structural opening reaction enters the rate expression as a pre-equilibrium step. The exchange rate of any hydrogen, k ex , is then determined by its chemical exchange rate in the open form, k ch , multiplied by the equilibrium opening constant, K op (Eq. 2).

Chromosome segregation during mitosis requires assembly of the kinetochore complex at the centromere. Key to kinetochore assembly is the specific recognition of the histone variant CENP-A in the centromeric nucleosome by centromere protein C (CENP-C). We have defined the determinants of this recognition mechanism and discovered that CENP-C binds a hydrophobic region in the CENP-A tail and docks onto the acidic patch of histone H2A/H2B. We further find that the more broadly conserved CENP-C motif uses the same mechanism for CENP-A nucleosome recognition. Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through nucleosome-docking-facilitated hydrophobic interactions.

The hydrogen exchange (HX) rates of the slowest peptide group NH hydrogens in oxidized cytochrome c (equine) are controlled by the transient global unfolding equilibrium. These rates can be measured by one-dimensional nuclear magnetic resonance and used to determine the thermodynamic parameters of global unfolding at mild solution conditions well below the melting transition. The free energy for global unfolding measured by hydrogen exchange can differ from values found by standard denaturation methods, most notably due to the slow cis-trans isomerization of the prolyl peptide bond. This difference can be quantitatively calculated from basic principles. Even with these corrections, HX experiments at low denaturant concentration measure a free energy of protein stability that rises above the usual linear extrapolation from denaturation data, as predicted by the denaturant binding model of Tanford.

Together with core histones, which make up the nucleosome, the linker histone (H1) is one of the five main histone protein families present in chromatin in eukaryotic cells. H1 binds to the nucleosome to form the next structural unit of metazoan chromatin, the chromatosome, which may help chromatin to fold into higher-order structures. Despite their important roles in regulating the structure and function of chromatin, linker histones have not been studied as extensively as core histones. Nevertheless, substantial progress has been made recently. The first near-atomic resolution crystal structure of a chromatosome core particle and an 11 Å resolution cryo-electron microscopy-derived structure of the 30 nm nucleosome array have been determined, revealing unprecedented details about how linker histones interact with the nucleosome and organize higher-order chromatin structures. Moreover, several new functions of linker histones have been discovered, including their roles in epigenetic regulation and the regulation of DNA replication, DNA repair and genome stability. Studies of the molecular mechanisms of H1 action in these processes suggest a new paradigm for linker histone function beyond its architectural roles in chromatin.

Kinetic and equilibrium isotope effects in peptide group hydrogen exchange reactions were evaluated. Unlike many other reactions, kinetic isotope effects in amide hydrogen exchange are small because exchange pathways are not limited by bond-breaking steps. Rate constants for the acid-catalyzed exchange of peptide group NH, ND, and NT in H2O are essentially identical, but a solvent isotope effect doubles the rate in D2O. Rate constants for base-catalyzed exchange in H2O decrease slowly in the order NH > ND > NT. The alkaline rate constant in D2O is very close to that in H2O when account is taken of the glass electrode pH artifact and the difference in solvent ionization constant. Small equilibrium isotope effects lead to an excess equilibrium accumulation of the heavier isotopes by the peptide group. Results obtained are expressed in terms of rate constants for the random coil polypeptide, poly-DL-alanine, to provide reference rates for protein hydrogen exchange studies as described in Bai et al. [preceding paper in this issued].

Summary Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses, previous cross-linking and fluorescence recovery after photobleach experiments, and helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures.

This discussion, prepared for the Protein Society's symposium honoring the 100th anniversary of Kaj Linderstr~m-Lang, shows how hydrogen exchange approaches initially conceived and implemented by Lang and his colleagues some 50 years ago are contributing to current progress in structural biology. Examples are chosen from the active protein folding field. Hydrogen exchange methods now make it possible to define the structure of protein folding intermediates in various contexts: as tenuous molten globule forms at equilibrium under destabilizing conditions, in kinetic intermediates that exist for less than one second, and as infinitesimally populated excited state forms under native conditions. More generally, similar methods now find broad application in studies of protein structure, energetics, and interactions. This article considers the rise of these capabilities from their inception at the Carlsberg Labs to their contemporary role as a significant tool of modem structural biology.Keywords: cooperativity; folding intermediates; hydrogen exchange; Linderstrom-Lang; molten globule; protein foldingThe hydrogen exchange approach was conceived by Kaj Linderstram-Lang and implemented by him and his collaborators at the Carlsberg laboratories in the early 1950s. Pauling had just discovered the a-helix and P-sheet and postulated that they were stabilized by hydrogen bonds. In those exciting days at the dawn of modem protein science, Lang realized that peptide group NH hydrogens participate in continual exchange with the hydrogens of solvent, just as in the already understood polar side chains. He set out to test Pauling's ideas by measuring the exchange behavior of these hydrogens. Lang created entirely novel methods to measure H-D exchange, and together with his colleagues at the Carlsberg Labs, he studied hydrogen exchange in a number of proteins and peptides under various solution conditions (Hvidt & LinderstrgmLang, 1954, 1955a, 1955b Krause & Linderstrom-Lang, 1955;Linderstrom-Lang, 1955a, 1955b Berger & Linderstram-Lang, 1957; Benson & Linderstmm-Lang, 1959; Hvidt et ai., 1960). In comparison with modem capabilities the information available to Lang was severely limited in resolution and even in accuracy. Remarkably, he saw past these limitations and quickly moved past