Hydrogen-deuterium exchange in the free and immunoglobulin G-bound protein G B-domain

Kinetic titration series with biolayer interferometry

Biolayer interferometry is a method to analyze protein interactions in real-time. In this study, we illustrate the usefulness to quantitatively analyze high affinity protein ligand interactions employing a kinetic titration series for characterizing the interactions between two pairs of interaction patterns, in particular immunoglobulin G and protein G B1 as well as scFv IC16 and amyloid beta (1-42). Kinetic titration series are commonly used in surface plasmon resonance and involve sequential injections of analyte over a desired concentration range on a single ligand coated sensor chip without waiting for complete dissociation between the injections. We show that applying this method to biolayer interferometry is straightforward and i) circumvents problems in data evaluation caused by unavoidable sensor differences, ii) saves resources and iii) increases throughput if screening a multitude of different analyte/ligand combinations.

Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein–ligand complexes

Ligand binding to a protein can elicit a wide range of responses when studied by HDX mass spectrometry.

Tracing primordial protein evolution through structurally guided stepwise segment elongation

The understanding of how primordial proteins emerged has been a fundamental and longstanding issue in biology and biochemistry. For a better understanding of primordial protein evolution, we synthesized an artificial protein on the basis of an evolutionary hypothesis, segment-based elongation starting from an autonomously foldable short peptide. A 10-residue protein, chignolin, the smallest foldable polypeptide ever reported, was used as a structural support to facilitate higher structural organization and gain-of-function in the development of an artificial protein. Repetitive cycles of segment elongation and subsequent phage display selection successfully produced a 25-residue protein, termed AF.2A1, with nanomolar affinity against the Fc region of immunoglobulin G. AF.2A1 shows exquisite molecular recognition ability such that it can distinguish conformational differences of the same molecule. The structure determined by NMR measurements demonstrated that AF.2A1 forms a globular protein-like conformation with the chignolin-derived β-hairpin and a tryptophan-mediated hydrophobic core. Using sequence analysis and a mutation study, we discovered that the structural organization and gain-of-function emerged from the vicinity of the chignolin segment, revealing that the structural support served as the core in both structural and functional development. Here, we propose an evolutionary model for primordial proteins in which a foldable segment serves as the evolving core to facilitate structural and functional evolution. This study provides insights into primordial protein evolution and also presents a novel methodology for designing small sized proteins useful for industrial and pharmaceutical applications.

Segmental polymorphism in a functional amyloid

Although amyloid fibrils are generally considered to be causative or contributing agents in amyloid diseases, several amyloid fibrils are also believed to have biological functions. Among these are fibrils formed by Pmel17 within melanosomes, which act as a template for melanin deposition. We use solid-state NMR to show that the molecular structures of fibrils formed by the 130-residue pseudo-repeat domain Pmel17:RPT are polymorphic even within the biologically relevant pH range. Thus, biological function in amyloid fibrils does not necessarily imply a unique molecular structure. Solid-state NMR spectra of three Pmel17:RPT polymorphs show that in all cases, only a subset (~30%) of the full amino acid sequence contributes to the immobilized fibril core. Although the repetitive nature of the sequence and incomplete spectral resolution prevent the determination of unique chemical shift assignments from two- and three-dimensional solid-state NMR spectra, we use a Monte Carlo assignment algorithm to identify protein segments that are present in or absent from the fibril core. The results show that the identity of the core-forming segments varies from one polymorph to another, a phenomenon known as segmental polymorphism.

A minimal sequence code for switching protein structure and function

We present here a structural and mechanistic description of how a protein changes its fold and function, mutation by mutation. Our approach was to create 2 proteins that (i) are stably folded into 2 different folds, (ii) have 2 different functions, and (iii) are very similar in sequence. In this simplified sequence space we explore the mutational path from one fold to another. We show that an IgG-binding, 4beta+alpha fold can be transformed into an albumin-binding, 3-alpha fold via a mutational pathway in which neither function nor native structure is completely lost. The stabilities of all mutants along the pathway are evaluated, key high-resolution structures are determined by NMR, and an explanation of the switching mechanism is provided. We show that the conformational switch from 4beta+alpha to 3-alpha structure can occur via a single amino acid substitution. On one side of the switch point, the 4beta+alpha fold is >90% populated (pH 7.2, 20 degrees C). A single mutation switches the conformation to the 3-alpha fold, which is >90% populated (pH 7.2, 20 degrees C). We further show that a bifunctional protein exists at the switch point with affinity for both IgG and albumin.

Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus

To determine whether the alpha-helix in the B3 immunoglobulin binding domain of protein G from group G Streptococcus has conformational stability as an isolated fragment, we carried out a CD and NMR study of the 16-residue peptide in solution corresponding to this alpha-helix. Based on two-dimensional H-NMR spectra recorded at three different temperatures (283, 305, and 313 K), it was found that this peptide is mostly unstructured in water at these temperatures. Weak signals corresponding to i,i+3 or i,i+4 interactions, which are characteristic of formation of turn-like structures, were observed in the ROE spectra at all temperatures. The absence of a stable three-dimensional structure of the investigated peptide supports an earlier study (Blanco and Serrano, Eur J Biochem 1995, 230, 634-649) of a possible mechanism for folding of other (B1 and B2) immunoglobulin binding domains of Protein G.

Ligation-state hydrogen exchange: coupled binding and folding equilibria in ribonuclease P protein

Bacillus subtilis ribonuclease P protein (P protein) is predominantly unfolded (D) at physiological pH and low ionic strength; however, small molecule anionic ligands (e.g., sulfate) directly bind to and stabilize the folded state (NL2). Because the D + 2L <--> NL2 transition is experimentally two-state, high-energy states such as the singly bound, folded species (NL) and the unliganded folded species (N) are generally difficult to detect at equilibrium. To study the conformational properties of these ensembles, NMR-detected amide hydrogen exchange (HX) rates of P protein were measured at four sulfate (i.e., ligand) concentrations, a method we denote "ligation-state hydrogen exchange". The ligand concentration dependence of the HX rate of 47 residues was fit to a model with four possible HX pathways, corresponding to the local and/or global opening reactions from NL2 and NL, the local opening of N, and the global opening of N to D. Data analysis permits the calculation of the residue-specific free energy of opening from each ensemble as well as the fractional amide HX flux through each pathway. Results indicate that the predominant route of HX is through the NL and N states, which represent only 0.45% and 0.0005% of the total protein population in 20 mM sodium sulfate, respectively. Despite the low population of N, a region of protected amides was identified. Therefore, exchange through unliganded forms must be accounted for prior to the interpretation of HX-based protein-interaction studies. We offer a simple test to determine if HX occurs through the liganded or unliganded form.

The design and characterization of two proteins with 88% sequence identity but different structure and function

To identify a simplified code for conformational switching, we have redesigned two natural proteins to have 88% sequence identity but different tertiary structures: a 3-alpha helix fold and an alpha/beta fold. We describe the design of these homologous heteromorphic proteins, their structural properties as determined by NMR, their conformational stabilities, and their affinities for their respective ligands: IgG and serum albumin. Each of these proteins is completely folded at 25 degrees C, is monomeric, and retains the native binding activity. The complete binding epitope for both ligands is encoded within each of the proteins. The IgG-binding epitope is functional only in the alpha/beta fold, and the albumin-binding epitope is functional only in the 3-alpha fold. These results demonstrate that two monomeric folds and two different functions can be encoded with only 12% of the amino acids in a protein (7 of 56). The fact that 49 aa in these proteins are compatible with both folds shows that the essential information determining a fold can be highly concentrated in a few amino acids and that a very limited subset of interactions in the protein can tip the balance from one monomer fold to another. This delicate balance helps explain why protein structure prediction is so challenging. Furthermore, because a few mutations can result in both new conformation and new function, the evolution of new folds driven by natural selection for alternative functions may be much more probable than previously recognized.

Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry

One advantage of detecting amide H/2H exchange by mass spectrometry instead of NMR is that the more rapidly exchanging surface amides are still detectable. In this study, we present quench-flow amide H/2H exchange experiments to probe how rapidly the surfaces of two different proteins exchange. We compared the amide H/2H exchange behavior of thrombin, a globular protein, and IkappaBalpha, a nonglobular protein, to explore any differences in the determinants of amide H/2H exchange rates for each class of protein. The rates of exchange of only a few of the surface amides were as rapid as the "intrinsic" exchange rates measured for amides in unstructured peptides. Most of the surface amides exchanged at a slower rate, despite the fact that they were not seen to be hydrogen bonded to another protein group in the crystal structure. To elucidate the influence of the surface environment on amide H/2H exchange, we compared exchange data with the number of amides participating in hydrogen bonds with other protein groups and with the solvent accessible surface area. The best correlation with amide H/2H exchange was found with the total solvent accessible surface area, including side chains. In the case of the globular protein, the correlation was modest, whereas it was well correlated for the nonglobular protein. The nonglobular protein also showed a correlation between amide exchange and hydrogen bonding. These data suggest that other factors, such as complex dynamic behavior and surface burial, may alter the expected exchange rates in globular proteins more than in nonglobular proteins where all of the residues are near the surface.

Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils

We describe solid-state nuclear magnetic resonance (NMR) measurements on fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)) that place constraints on the identity and symmetry of contacts between in-register, parallel beta-sheets in the fibrils. We refer to these contacts as internal and external quaternary contacts, depending on whether they are within a single molecular layer or between molecular layers. The data include (1) two-dimensional 13C-13C NMR spectra that indicate internal quaternary contacts between side chains of L17 and F19 and side chains of I32, L34, and V36, as well as external quaternary contacts between side chains of I31 and G37; (2) two-dimensional 15N-13C NMR spectra that indicate external quaternary contacts between the side chain of M35 and the peptide backbone at G33; (3) measurements of magnetic dipole-dipole couplings between the side chain carboxylate group of D23 and the side chain amine group of K28 that indicate salt bridge interactions. Isotopic dilution experiments allow us to make distinctions between intramolecular and intermolecular contacts. On the basis of these data and previously determined structural constraints from solid-state NMR and electron microscopy, we construct full molecular models using restrained molecular dynamics simulations and restrained energy minimization. These models apply to Abeta(1-40) fibrils grown with gentle agitation. We also present evidence for different internal quaternary contacts in Abeta(1-40) fibrils grown without agitation, which are morphologically distinct.

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

A continuum electrostatics approach for molecular dynamics (MD) simulations of macromolecules is presented and analyzed for its performance on a peptide and a globular protein. The approach incorporates the screened Coulomb potential (SCP) continuum model of electrostatics, which was reported earlier. The model was validated in a broad set of tests some of which were based on Monte Carlo simulations that included single amino acids, peptides, and proteins. The implementation for large-scale MD simulations presented in this article is based on a pairwise potential that makes the electrostatic model suitable for fast analytical calculation of forces. To assess the suitability of the approach, a preliminary validation is conducted, which consists of (i) a 3-ns MD simulation of the immunoglobulin-binding domain of streptococcal protein G, a 56-residue globular protein and (ii) a 3-ns simulation of Dynorphin, a biological peptide of 17 amino acids. In both cases, the results are compared with those obtained from MD simulations using explicit water (EW) molecules in an all-atom representation. The initial structure of Dynorphin was assumed to be an alpha-helix between residues 1 and 9 as suggested from NMR measurements in micelles. The results obtained in the MD simulations show that the helical structure collapses early in the simulation, a behavior observed in the EW simulation and consistent with spectroscopic data that suggest that the peptide may adopt mainly an extended conformation in water. The dynamics of protein G calculated with the SCP implicit solvent model (SCP-ISM) reveals a stable structure that conserves all the elements of secondary structure throughout the entire simulation time. The average structures calculated from the trajectories with the implicit and explicit solvent models had a cRMSD of 1.1 A, whereas each average structure had a cRMSD of about 0.8A with respect to the X-ray structure. The main conformational differences of the average structures with respect to the crystal structure occur in the loop involving residues 8-14. Despite the overall similarity of the simulated dynamics with EW and SCP models, fluctuations of side-chains are larger when the implicit solvent is used, especially in solvent exposed side-chains. The MD simulation of Dynorphin was extended to 40 ns to study its behavior in an aqueous environment. This long simulation showed that the peptide has a tendency to form an alpha-helical structure in water, but the stabilization free energy is too weak, resulting in frequent interconversions between random and helical conformations during the simulation time. The results reported here suggest that the SCP implicit solvent model is adequate to describe electrostatic effects in MD simulation of both peptides and proteins using the same set of parameters. It is suggested that the present approach could form the basis for the development of a reliable and general continuum approach for use in molecular biology, and directions are outlined for attaining this long-term goal.

The role of backbone conformational heat capacity in protein stability: temperature dependent dynamics of the B1 domain of Streptococcal protein G

The contributions of backbone NH group dynamics to the conformational heat capacity of the B1 domain of Streptococcal protein G have been estimated from the temperature dependence of 15N NMR-derived order parameters. Longitudinal (R1) and transverse (R2) relaxation rates, transverse cross-relaxation rates (eta(xy)), and steady state [1H]-15N nuclear Overhauser effects were measured at temperatures of 0, 10, 20, 30, 40, and 50 degrees C for 89-100% of the backbone secondary amide nitrogen nuclei in the B1 domain. The ratio R2/eta(xy) was used to identify nuclei for which conformational exchange makes a significant contribution to R2. Relaxation data were fit to the extended model-free dynamics formalism, incorporating an axially symmetric molecular rotational diffusion tensor. The temperature dependence of the order parameter (S2) was used to calculate the contribution of each NH group to conformational heat capacity (Cp) and a characteristic temperature (T*), representing the density of conformational energy states accessible to each NH group. The heat capacities of the secondary structure regions of the B1 domain are significantly higher than those of comparable regions of other proteins, whereas the heat capacities of less structured regions are similar to those in other proteins. The higher local heat capacities are estimated to contribute up to approximately 0.8 kJ/mol K to the total heat capacity of the B1 domain, without which the denaturation temperature would be approximately 9 degrees C lower (78 degrees C rather than 87 degrees C). Thus, variation of backbone conformational heat capacity of native proteins may be a novel mechanism that contributes to high temperature stabilization of proteins.

Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature

Rubredoxin from the hyperthermophile Pyrococcus furiosus is the most thermostable protein characterized to date with an estimated global unfolding rate of 10(-6) s(-1) at 100 degrees C. In marked contrast to these slow global dynamics, hydrogen exchange experiments here demonstrate that conformational opening for solvent access occurs in the approximately millisecond time frame or faster at 28 degrees C for all amide positions. Under these conditions all backbone amides with exchange protection factors between 10(4) and 10(6), for which EX(2) exchange kinetics were directly verified, have exchange activation energy values within 2-3 kcal/mol of that observed for unstructured peptides. The conformational flexibility of this protein is thus sufficient for water and base catalyst access to the exchanging amide with quite limited structural disruption. The common hypothesis that enhanced conformational rigidity in the folded native state underlies the increased thermal stability of hyperthermophile proteins is not supported by these data.

Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature

Rubredoxin from the hyperthermophile Pyrococcus furiosus is the most thermostable protein characterized to date with an estimated global unfolding rate of 10(-6) s(-1) at 100 degrees C. In marked contrast to these slow global dynamics, hydrogen exchange experiments here demonstrate that conformational opening for solvent access occurs in the approximately millisecond time frame or faster at 28 degrees C for all amide positions. Under these conditions all backbone amides with exchange protection factors between 10(4) and 10(6), for which EX(2) exchange kinetics were directly verified, have exchange activation energy values within 2-3 kcal/mol of that observed for unstructured peptides. The conformational flexibility of this protein is thus sufficient for water and base catalyst access to the exchanging amide with quite limited structural disruption. The common hypothesis that enhanced conformational rigidity in the folded native state underlies the increased thermal stability of hyperthermophile proteins is not supported by these data.

Synthesis, folding, and structure of the beta-turn mimic modified B1 domain of streptococcal protein G

The mechanism of beta-sheet formation remains a fundamental issue in our understanding of the protein folding process, but is hampered by the often encountered kinetic competition between folding and aggregation. The role of local versus nonlocal interactions has been probed traditionally by mutagenesis of both turn and strand residues. Recently, rigid organic molecules that impose a correct chain reversal have been introduced in several small peptides to isolate the importance of the long-range interactions. Here, we present the incorporation of a well-studied beta-turn mimic, designated as the dibenzofuran-based (DBF) amino acid, in the B1 domain of streptococcal protein G (B1G), and compare our results with those obtained upon insertion of the same mimic into the N-terminal beta-hairpin of B1G (O Melnyk et al., 1998, Lett Pept Sci 5:147-150). The DBF-B1G domain conserves the structure and the functional and thermodynamical properties of the native protein, whereas the modified peptide does not adopt a native-like conformation. The nature of the DBF flanking residues in the modified B1G domain prevents the beta-turn mimic from acting as a strong beta-sheet nucleator, which reinforces the idea that the native beta-hairpin formation is not driven by the beta-turn formation, but by tertiary interactions.

Identification of protein-protein interfaces by decreased amide proton solvent accessibility

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. The protein-protein interface was reliably indicated by those peptides that retained more deuterons in the complex compared with control experiments in which only one protein was present. The method was used to identify the kinase inhibitor [PKI(5-24)] and ATP-binding sites in the cyclic-AMP-dependent protein kinase. Three overlapping peptides identified the ATP-binding site, three overlapping peptides identified the glycine-rich loop, and two peptides identified the PKI(5-24)-binding site. A complex of unknown structure also was analyzed, human alpha-thrombin bound to an 83-aa fragment of human thrombomodulin [TMEGF(4-5)]. Five peptides from thrombin showed significantly decreased solvent accessibility in the complex. Three peptides identified the anion-binding exosite I, confirming ligand competition experiments. Two peptides identified a new region of thrombin near the active site providing a potential mechanism of how thrombomodulin alters thrombin substrate specificity.

Hydrogen exchange and protein folding

Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.

Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200 degrees C

The rubredoxin protein from the hyperthermophilic archaebacterium Pyrococcus furiosus was examined by a hydrogen exchange method. Even though the protein does not exhibit reversible thermal unfolding, one can determine its stability parameters-free energy, enthalpy, entropy, and melting temperature-and also the distribution of stability throughout the protein, by using hydrogen exchange to measure the reversible cycling of the protein between native and unfolded states that occurs even under native conditions.

A molecular dynamics simulation study of segment B1 of protein G

The immunoglobulin binding protein, segment B1 of protein G, has been studied experimentally as a paradigm for protein folding. This protein consists of 56 residues, includes both beta sheet and alpha helix and contains neither disulfide bonds nor proline residues. We report an all-atom molecular dynamics study of the native manifold of the protein in explicit solvent. A 2-ns simulation starting from the nuclear magnetic resonance (NMR) structure and a 1-ns control simulation starting from the x-ray structure were performed. The difference between average structures calculated over the equilibrium portion of trajectories is smaller than the difference between their starting conformations. These simulation averages are structurally similar to the x-ray structure and differ in systematic ways from the NMR-determined structure. Partitioning of the fluctuations into fast (< 20 ps) and slow (> 20 ps) components indicates that the beta sheet displays greater long-time mobility than does the alpha helix. Clore and Gronenborn [J. Mol. Biol. 223:853-856, 1992] detected two long-residence water molecules by NMR in a solution structure of segment B1 of protein G. Both molecules were found in the fully exposed regions and were proposed to be stabilized by bifurcated hydrogen bonds to the protein backbone. One of these long-residence water molecules, found near an exposed loop region, is identified in both of our simulations, and is seen to be involved in the formation of a stable water-mediated hydrogen bond bridge. The second water molecule, located near the middle of the alpha helix, is not seen with an exceptional residence time in either as a result of the conformation being closer to the x-ray structure in this region of the protein.

Ligand binding to proteins: the binding landscape model

Models of ligand binding are often based on four assumptions: (1) steric fit: that binding is determined mainly by shape complementarity; (2) native binding: that ligands mainly bind to native states; (3) locality: that ligands perturb protein structures mainly at the binding site; and (4) continuity: that small changes in ligand or protein structure lead to small changes in binding affinity. Using a generalization of the 2D HP lattice model, we study ligand binding and explore these assumptions. We first validate the model by showing that it reproduces typical binding behaviors. We observe ligand-induced denaturation, ANS and heme-like binding, and "lock-and-key" and "induced-fit" specific binding behaviors characterized by Michaelis-Menten or more cooperative types of binding isotherms. We then explore cases where the model predicts violations of the standard assumptions. For example, very different binding modes can result from two ligands of identical shape. Ligands can sometimes bind highly denatured states more tightly than native states and yet have Michaelis-Menten isotherms. Even low-population binding to denatured states can cause changes in global stability, hydrogen-exchange rates, and thermal B-factors, contrary to expectations, but in agreement with experiments. We conclude that ligand binding, similar to protein folding, may be better described in terms of energy landscapes than in terms of simpler mass-action models.

Reduction in the amide hydrogen exchange rates of an anti-lysozyme Fv fragment due to formation of the Fv-lysozyme complex

The Fv fragment of the monoclonal antibody D1.3 was expressed in bacteria. Standard triple resonance techniques were used to obtain the NMR resonance assignments for 211 out of 215 backbone 15N/NH atoms for D1.3 Fv. Using these assignments, hydrogen exchange rates are measured for 82 amide hydrogen atoms in D1.3 Fv free and bound to hen egg-white lysozyme. Upon binding to antigen, exchange rates are decreased for residues throughout the Fv. Many of these residues are located remote from the site of interaction with the antigen. These changes are larger than previously observed for the antigen portion of the complex. Evidently, the beta-sheet structure of the Fv propagates the effects of binding more efficiently than the antigen. These effects are compared between the three different polypeptide chains that make up the complex. These data suggest that reduced dynamics are a general feature of antibody binding to antigen.

Hydrogen exchange: the modern legacy of Linderstrøm-Lang

This discussion, prepared for the Protein Society's symposium honoring the 100th anniversary of Kaj Linderstrøm-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 modern structural biology.

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain

The albumin-binding GA module is found in a family of surface proteins of different bacterial species. It comprises 45 amino acid residues and represents the first known example of contemporary module shuffling. Using 1H NMR spectroscopy we have determined the solution structure of the GA module from protein PAB, a protein of the anaerobic human commensal and pathogen Peptostreptococcus magnus. This structure, the first three-dimensional structure of an albumin-binding protein domain described, was shown to be composed of a left-handed three-helix-bundle. Sequence differences between GA modules with different affinities for albumin indicated that a conserved region in the C-terminal part of the second helix and the flexible sequence between helices 2 and 3 could contribute to the albumin-binding activity. The effect on backbone amide proton exchange rates upon binding to albumin support this assumption. The GA module has a fold that is strikingly similar to the immunoglobulin-binding domains of staphylococcal protein A but it shows no resemblance to the fold shared by the immunoglobulin-binding domains of streptococcal protein G and peptostreptococcal protein L. When the gene sequences, binding properties and thermal stability of these four domains are analysed in relation to their global folds an evolutionary pattern emerges. Thus, in the evolution of novel binding properties mutations are allowed only as long as the energetically favourable global fold is maintained.

Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the alpha-helix fragment

BACKGROUND

The role of local interactions in protein folding and stability can be investigated by the conformational analysis of protein fragments. The hydrophobic staple and Schellman motifs have been described at the N and C terminus, respectively, of protein alpha-helices. These motifs are characterized by an interaction between two hydrophobic residues, one outside the helix and one within the helix, and their importance for helix stability has been analyzed in model peptides. In the alpha-helix of the protein G B1 domain, only the Schellman motif is formed--the hydrophobic staple motif is absent despite the favourable sequence pattern. We have experimentally analyzed the solution conformation of the 19-41 fragment of protein G. This peptide comprises the helical residues and contains both the hydrophobic staple and Schellman motif sequences.

RESULTS

In the isolated peptide in water, the hydrophobic staple motif is formed and stabilizes the helical structure as compared with a shorter peptide lacking it, but the Schellman motif is not formed. In 30% aqueous TFE, the helix is more stable than in pure water and both motifs are formed.

CONCLUSIONS

The results suggest that the importance of each motif for the folding and stability of protein G is different. The nonnative hydrophobic staple interaction can help to nucleate the helix at the beginning of folding but has later to be disrupted. The Schellman motif, while not providing enough energy for substantial helix stabilization in the unfolded state, could be important for determining the local fold of the sequence in the context of the rest of the protein.

Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH

Despite the general observation that single domain proteins denature in a completely cooperative manner, amide hydrogen exchange of ribonuclease H in low levels of denaturant demonstrates the existence of two partially folded species. The structures of these marginally stable species resemble kinetic folding intermediates and the molten globule state of the protein. These data suggest that the first region to fold is the thermodynamically most stable portion of the protein and that the molten globule is a high free energy conformation present at equilibrium in the native state.

Protein complexes studied by NMR spectroscopy

Recent advances in NMR methods now allow protein complexes to be studied in great detail in a wide range of solution conditions. Isotope-enrichment strategies, resonance-assignment approaches and structural-determination methods have evolved to the point where almost any type of complex involving proteins of reasonable size may be studied in a straightforward way. A variety of isotope editing and filtering strategies underlie these powerful methodologies. Approaches to the characterization of the dynamics of protein complexes have also matured to the point where detailed studies of the effects of complexation on dynamics can be studied over a wide range of timescales.

Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR

We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates.

Backbone dynamics of a domain of protein L which binds to immunoglobulin light chains

Protein L is a multidomain protein expressed at the surface of some strains of the anaerobic bacterial species Peptostreptococcus magnus. The molecule interacts with the variable domain of immunoglobulin (Ig) light chains through five repeated homologous domains denoted B1 to B5. The fold of the Ig-light-chain-binding B1 domain of protein L (PLB1) has been shown to comprise an alpha-helix packed against a four-stranded beta-sheet and therefore resembles the structure of the IgG-binding domains of streptococcal protein G. In the present study, amide-proton exchange and 15N-relaxation NMR measurements were performed on the B1 domain to investigate its backbone mobility. It was shown that the folded portion of PLB1 is rigid with no regions of significantly higher flexibility than average. The N-terminus, however, is highly flexible consistent with earlier studies on the solution structure of PLB1. Comparison of the amide-proton-exchange data with similar measurements performed on the IgG-binding domains of protein G indicates that the two proteins have different exchange behaviors in their second beta-strands. Both protein G and L employ this region of their structures for binding to immunoglobulins since the interaction of protein G and protein L with IgG Fab and the Ig light chain, respectively, involves residues from the second beta-strand.

Mechanisms and uses of hydrogen exchange

Recent work has largely completed our understanding of the hydrogen-exchange chemistry of unstructured proteins and nucleic acids. Some of the high-energy structural fluctuations that determine the hydrogen-exchange behavior of native macromolecules have been explained; others remain elusive. A growing number of applications are exploiting hydrogen-exchange behavior to study difficult molecular systems and elicit otherwise inaccessible information on protein structure, dynamics and energetics.

Equilibrium and pre-equilibrium fluorescence spectroscopic studies of the binding of a single-immunoglobulin-binding domain derived from protein G to the Fc fragment from human IgG1

A single-immunoglobulin-binding protein based upon the C2 domain of Protein G from Streptococcus has been shown to bind tightly to the Fc fragment of IgG1. The binding interaction results in a decrease in the fluorescence intensity from the sole Trp residue (Trp-48) in this domain. This spectral change has been used to monitor the binding interactions between the two proteins using equilibrium and pre-equilibrium fluorescence spectroscopy. Comparison of the data from the two techniques suggests that a conformational change occurs after the initial formation of the complex. Mutagenesis studies have shown that the Trp residue is important for binding and that replacement by a Phe residue is important for binding and that replacement by a Phe residue leads to a 300-fold decrease in the affinity for Fc gamma 1. Determination of the rate constants kon and koff at different values of pH between 4.0 and 9.0 suggest that variations in Kd are mediated predominantly by changes in kon. Competition experiments between SpG1 and a single-IgG-binding domain from Protein A from Staphylococcus aureus have been used to determine the affinity of the latter for Fc gamma 1.

Structures of bacterial immunoglobulin-binding domains and their complexes with immunoglobulins

Three-dimensional structures are now available for several immunoglobulin binding domains from bacterial proteins A, G, and L. X-ray diffraction and NMR experiments on complexes of these domains with portions of immunoglobulins have revealed common structural themes used in these interactions. These data expand our understanding of structure/function relationships in these molecular recognition processes and provide the basis for rational design of artificial immunoglobulin-binding molecules.

Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements

The solution structure of the isolated fragments 1-20 (beta-hairpin), 21-40 (alpha-helix) and 41-56 (beta-hairpin), corresponding to all the secondary structure elements of the protein G B1 domain, have been studied by circular dichroism and nuclear magnetic resonance techniques. In the protein G B1-(1-20) fragment turn-like folded structures were detected in water though low populated. In the presence of 30% aqueous trifluoroethanol there is a complex conformational behaviour in which a helical structure at the N-terminal half is formed in equilibrium with random and native-like beta-hairpin structures. The peptide corresponding to the alpha-helix is predominantly unstructured in water, while in 30% trifluoroethanol it highly populates a native alpha-helical conformation, including a (i,i + 5) interaction between hydrophobic residues at its C-terminus. The third peptide was previously reported to form a monomeric native beta-hairpin structure in water [Blanco, F. J., Rivas, G. & Serrano, L. (1994a) Nature Struc. Biol. 1, 584-590]. We show in this work that the beta-hairpin structure is further stabilized in 30% trifluoroethanol and destabilised in the presence of 6 M urea, though some folded structure persists even in these highly denaturing conditions. The conformational properties of these peptides suggests that the second beta-hairpin could be an important folding initiation site on which the rest of the chain folds. Reconstitution experiments failed to show evidence of interaction between the peptides. Algorithms designed to predict the helical and extended conformations of peptides in aqueous solution successfully describe the complicated behaviour of these peptides. Comparison of the predicted and the experimental results with those for a structurally related protein, ubiquitin, shows very strong similarities, the main difference being the switch of the most stable beta-hairpin from the N-terminus in ubiquitin to the C-terminus in protein G.