Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices

Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices

The single alpha helix (SAH) is a recurring motif in biology. The consensus sequence has a di-block architecture that includes repeats of four consecutive glutamate residues followed by four consecutive lysine residues. Measurements show that the overall helicity of sequences with consensus E4 K4 repeats is insensitive to a wide range of pH values. Here, we use the recently introduced q-canonical ensemble, which allows us to decouple measurements of charge state and conformation, to explain the observed insensitivity of SAH helicity to pH. We couple the outputs from separate measurements of charge and conformation with atomistic simulations to derive residue-specific quantifications of preferences for being in an alpha helix and for the ionizable residues to be charged vs. uncharged. We find a clear preference for accommodating uncharged Glu residues within internal positions of SAH-forming sequences. The stabilities of alpha helical conformations increase with the number of E4 K4 repeats and so do the numbers of accessible charge states that are compatible with forming conformations of high helical content. There is conformational buffering whereby charge state heterogeneity buffers against large-scale conformational changes thus making the overall helicity insensitive to large changes in pH. Further, the results clearly argue against a single, rod-like alpha helical conformation being the only or even dominant conformation in the ensembles of so-called SAH sequences.

Bicyclic Schellman Loop Mimics (BSMs): Rigid Synthetic C-Caps for Enforcing Peptide Helicity

Macrocyclic peptides are the prevalent way to mimic interface helices for disruption of protein interactions, but current strategies to do this via synthetic C-cap mimics are underdeveloped and suboptimal. Bioinformatic studies described here were undertaken to better understand Schellman loops, the most common C-caps in proteins, to design superior synthetic mimics. An algorithm (Schellman Loop Finder) was developed, and data mining with this led to the discovery that these secondary structures are often stabilized by combinations of three hydrophobic side chains, most frequently from Leu, to form hydrophobic triangles. That insight facilitated design of synthetic mimics, bicyclic Schellman loop mimics (BSMs), where the hydrophobic triumvirate was replaced by 1,3,5-trimethylbenzene. We demonstrate that BSMs can be made quickly and efficiently, and are more rigid and helix-inducing than the best current C-cap mimics, which are rare and all monocycles.

Selective recognition of N4-methylcytosine in DNA by engineered transcription-activator-like effectors

The epigenetic DNA nucleobases 5-methylcytosine (5mC) and N4-methylcytosine (4mC) coexist in bacterial genomes and have important functions in host defence and transcription regulation. To better understand the individual biological roles of both methylated nucleobases, analytical strategies for distinguishing unmodified cytosine (C) from 4mC and 5mC are required. Transcription-activator-like effectors (TALEs) are programmable DNA-binding repeat proteins, which can be re-engineered for the direct detection of epigenetic nucleobases in user-defined DNA sequences. We here report the natural, cytosine-binding TALE repeat to not strongly differentiate between 5mC and 4mC. To engineer repeats with selectivity in the context of C, 5mC and 4mC, we developed a homogeneous fluorescence assay and screened a library of size-reduced TALE repeats for binding to all three nucleobases. This provided insights into the requirements of size-reduced TALE repeats for 4mC binding and revealed a single mutant repeat as a selective binder of 4mC. Employment of a TALE with this repeat in affinity enrichment enabled the isolation of a user-defined DNA sequence containing a single 4mC but not C or 5mC from the background of a bacterial genome. Comparative enrichments with TALEs bearing this or the natural C-binding repeat provides an approach for the complete, programmable decoding of all cytosine nucleobases found in bacterial genomes.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.

Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases

The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature. We further show that fusion of TPR(2-142) to the MET intracellular domain strongly and selectively stabilizes the αG helix of the MET kinase domain, and mutations of only the TPR leucine zipper residues at the junction to MET, but not other leucine zipper residues, abolish kinase activation. Together, these results provide critical insight into the TPR structure and its ability to induce dimerization and activation of fusion kinases.

Interrogating Key Positions of Size-Reduced TALE Repeats Reveals a Programmable Sensor of 5-Carboxylcytosine

Transcription-activator-like effector (TALE) proteins consist of concatenated repeats that recognize consecutive canonical nucleobases of DNA via the major groove in a programmable fashion. Since this groove displays unique chemical information for the four human epigenetic cytosine nucleobases, TALE repeats with epigenetic selectivity can be engineered, with potential to establish receptors for the programmable decoding of all human nucleobases. TALE repeats recognize nucleobases via key amino acids in a structurally conserved loop whose backbone is positioned very close to the cytosine 5-carbon. This complicates the engineering of selectivities for large 5-substituents. To interrogate a more promising structural space, we engineered size-reduced repeat loops, performed saturation mutagenesis of key positions, and screened a total of 200 repeat-nucleobase interactions for new selectivities. This provided insight into the structural requirements of TALE repeats for affinity and selectivity, revealed repeats with improved or relaxed selectivity, and resulted in the first selective sensor of 5-carboxylcytosine.

Mapping side chain interactions at protein helix termini

Background

Interactions that involve one or more amino acid side chains near the ends of protein helices stabilize helix termini and shape the geometry of the adjacent loops, making a substantial contribution to overall protein structure. Previous work has identified key helix-terminal motifs, such as Asx/ST N-caps, the capping box, and hydrophobic and electrostatic interactions, but important questions remain, including: 1) What loop backbone geometries are favoured by each motif? 2) To what extent are multi-amino acid motifs likely to represent genuine cooperative interactions? 3) Can new motifs be identified in a large, recent dataset using the latest bioinformatics tools?

Results

Three analytical tools are applied here to answer these questions. First, helix-terminal structures are partitioned by loop backbone geometry using a new 3D clustering algorithm. Next, Cascade Detection, a motif detection algorithm recently published by the author, is applied to each cluster to determine which sequence motifs are overrepresented in each geometry. Finally, the results for each motif are presented in a CapMap, a 3D conformational heatmap that displays the distribution of the motif’s overrepresentation across loop geometries, enabling the rapid isolation and characterization of the associated side chain interaction. This work identifies a library of geometry-specific side chain interactions that provides a new, detailed picture of loop structure near the helix terminus. Highlights include determinations of the favoured loop geometries for the Asx/ST N-cap motifs, capping boxes, “big” boxes, and other hydrophobic, electrostatic, H-bond, and pi stacking interactions, many of which have not been described before.

Conclusions

This work demonstrates that the combination of structural clustering and motif detection in the sequence space can efficiently identify side chain motifs and map them to the loop geometries which they support. Protein designers should find this study useful, because it identifies side chain interactions which are good candidates for inclusion in synthetic helix-terminal loops with specific desired geometries, since they are used in nature to support these geometries. The techniques described here can also be applied to map side chain interactions associated with other structural components of proteins such as beta and gamma turns.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0671-4) contains supplementary material, which is available to authorized users.

The intrinsic disorder alphabet. III. Dual personality of serine

Proteins are natural polypeptides consisting of 20 major amino acid residues, content and order of which in a given amino acid sequence defines the ability of a related protein to fold into unique functional state or to stay intrinsically disordered. Amino acid sequences code for both foldable (ordered) proteins/domains and for intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), but these sequence codes are dramatically different. This difference starts with a very general property of the corresponding amino acid sequences, namely, their compositions. IDPs/IDPRs are enriched in specific disorder-promoting residues, whereas amino acid sequences of ordered proteins/domains typically contain more order-promoting residues. Therefore, the relative abundances of various amino acids in ordered and disordered proteins can be used to scale amino acids according to their disorder promoting potentials. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and represents serine, which is the third most disorder-promoting residue. Similar to previous publications, this review represents some physico-chemical properties of serine and the roles of this residue in structures and functions of ordered proteins, describes major posttranslational modifications tailored to serine, and finally gives an overview of roles of serine in structure and functions of intrinsically disordered proteins.

The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.

Caveolin-Na/K-ATPase interactions: role of transmembrane topology in non-genomic steroid signal transduction

Progesterone and its polar metabolite(s) trigger the meiotic divisions in the amphibian oocyte through a non-genomic signaling system at the plasma membrane. Published site-directed mutagenesis studies of ouabain binding and progesterone-ouabain competition studies indicate that progesterone binds to a 23 amino acid extracellular loop of the plasma membrane α-subunit of Na/K-ATPase. Integral membrane proteins such as caveolins are reported to form Na/K-ATPase-peptide complexes essential for signal transduction. We have characterized the progesterone-induced Na/K-ATPase-caveolin (CAV-1)-steroid 5α-reductase interactions initiating the meiotic divisions. Peptide sequence analysis algorithms indicate that CAV-1 contains two plasma membrane spanning helices, separated by as few as 1-2 amino acid residues at the cell surface. The CAV-1 scaffolding domain, reported to interact with CAV-1 binding (CB) motifs in signaling proteins, overlaps transmembrane (TM) helix 1. The α-subunit of Na/K-ATPase (10 TM helices) contains double CB motifs within TM-1 and TM-10. Steroid 5α-reductase (6 TM helices), an initial step in polar steroid formation, contains CB motifs overlapping TM-1 and TM-6. Computer analysis predicts that interaction between antipathic strands may bring CB motifs and scaffolding domains into close proximity, initiating allostearic changes. Progesterone binding to the α-subunit may thus facilitate CB motif:CAV-1 interaction, which in turn induces helix-helix interaction and generates both a signaling cascade and formation of polar steroids.

Coiled coils and SAH domains in cytoskeletal molecular motors

Cytoskeletal motors include myosins, kinesins and dyneins. Myosins move along tracks of actin filaments, whereas kinesins and dyneins move along microtubules. Many of these motors are involved in trafficking cargo in cells. However, myosins are mostly monomeric, whereas kinesins are mostly dimeric, owing to the presence of a coiled coil. Some myosins (myosins 6, 7 and 10) contain an SAH (single α-helical) domain, which was originally thought to be a coiled coil. These myosins are now known to be monomers, not dimers. The differences between SAH domains and coiled coils are described and the potential roles of SAH domains in molecular motors are discussed.

CAPS-DB: a structural classification of helix-capping motifs

The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (ϕ–ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. The database is accessible at: http://www.bioinsilico.org/CAPSDB.

Equilibrium and kinetic studies of protein cooperativity using urea-induced folding/unfolding of a Ubq-UIM fusion protein

Understanding the origins of cooperativity in proteins remains an important topic in protein folding. This study describes experimental folding/unfolding equilibrium and kinetic studies of the engineered protein Ubq-UIM, consisting of ubiquitin (Ubq) fused to the sequence of the ubiquitin interacting motif (UIM) via a short linker. Urea-induced folding/unfolding profiles of Ubq-UIM were monitored by far-UV circular dichroism and fluorescence spectroscopies and compared to those of the isolated Ubq domain. It was found that the equilibrium data for Ubq-UIM is inconsistent with a two-state model. Analysis of the kinetics of folding shows similarity in the folding transition state ensemble between Ubq and Ubq-UIM, suggesting that formation of Ubq domain is independent of UIM. The major contribution to the stabilization of Ubq-UIM, relative to Ubq, was found to be in the rates of unfolding. Moreover, it was found that the kinetic m-values for Ubq-UIM unfolding, monitored by different probes (far-UV circular dichroism and fluorescence spectroscopies), are different; thereby, further supporting deviations from a two-state behavior. A thermodynamic linkage model that involves four states was found to be applicable to the urea-induced unfolding of Ubq-UIM, which is in agreement with the previous temperature-induced unfolding study. The applicability of the model was further supported by site-directed variants of Ubq-UIM that have altered stabilities of Ubq/UIM interface and/or stabilities of individual Ubq- and UIM-domains. All variants show increased cooperativity and one variant, E43N_Ubq-UIM, appears to behave very close to an equilibrium two-state.

Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase

A rare Gly210 deletion in protoporphyrinogen oxidase (PPO) was recently discovered in herbicide-resistant Amaranthus tuberculatus. According to the published X-ray structure of Nicotiana tabacum PPO, Gly210 is adjacent to, not in, the PPO active site, so it is a matter of interest to determine why its deletion imparts resistance to herbicides. In our kinetic experiments, this deletion did not affect the affinity of protoporphyrinogen IX nor the FAD content, but decreased the catalytic efficiency of the enzyme. The suboptimal Kcat was compensated by a significant increase in the Kis for inhibitors and a switch in their interactions from competitive to mixed-type inhibition. In our protein modeling studies on herbicide-susceptible PPO and resistant PPO, we show that Gly210 plays a key role in the alphaL helix-capping motif at the C-terminus of the alpha-8 helix which helps to stabilize the helix. In molecular dynamics simulations, the deletion had significant architecture consequences, destabilizing the alpha-8 helix-capping region and unraveling the last turn of the helix, leading to enlargement of the active site cavity by approximately 50%. This seemingly innocuous deletion of Gly210 of the mitochondrial PPO imparts herbicide resistance to this dual-targeted protein without severely affecting its normal physiological function, which may explain why this unusual mutation was the favored evolutionary path for achieving resistance to PPO inhibitors.

Importance of the C-terminal loop L137-S141 for the folding and folding stability of staphylococcal nuclease

The role of the C-terminal loop L137-S141 in the folding and folding stability of staphylococcal nuclease (SNase) was investigated by deletion mutation. The C-terminal truncated SNase fragments, SNase137, SNase139, SNase140, and SNase141 containing residues 1-137, 1-139, 1-140, and 1-141, respectively, were adopted in this study. Folding states of these four SNase fragments were analyzed by circular dichroism and fluorescence measurements. The solution structure of SNase140 was determined and compared to those of SNase141 and native SNase using the heteronuclear NMR method. The results showed that folding of the four SNase fragments is correlated with the folding of helix alpha3. With the chain length extending from L137 and I139 to S141, folding of the fragments progressively approached to the tertiary folding of native SNase, and the folding stability was enhanced. These observations revealed that the C-terminal loop L137-S141 has profound effect not only on the folding of helix alpha3 but also on the stabilizing folding of both the alpha- and beta-subdomains of SNase. Analysis indicates that stabilizing folding of the SNase and SNase fragments depends to a large extent on the hydrophobic packing interactions in both the C-terminal local structural region surrounding W140 including the loop L137-S141 and the N-terminal local structural region of the "beta-barrel" hydrophobic core.

Residue patterning in helix interiorsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process

The α-helix remains a focus of research because of its importance to protein folding and structure. Nevertheless, despite numerous empirical, computational, and theoretical studies, the fundamental structural properties governing their formation and stability are still unclear. We have examined the statistical occurrence of polar and apolar residue patterning in helical interiors in a large, non-redundant dataset, and compared these patterns with those found in other structural environments. While the familiar amphipathic distributions for both polar and apolar residues are evident, our analysis also finds significant differences between these distributions. Non-amphipathic signals can also be discerned within both distributions. Most interestingly, among various positional patterning, an analysis of immediate (i,i + 1) helical neighbours found: (i) clear neighbouring preferences, with high (low) occurrences of hydrophobics (hydrophilics) next to Gly, Pro, and short polar residues; (ii) high negative (positive) correlation between residue helical propensities and the degree of neighbouring hydrophobicity (hydrophilicity); and (iii) a preferred ordering among neighbours, implying an inherent helix directionality. Because (i,i + 1) helical pairs have limited side chain – side chain interactions, thermodynamic considerations cannot readily explain these observations, nor can evolutionary pressures that enhance tertiary interactions via amphipathicity, as this particular spacing does not segregate residues onto either the same or opposing helical faces. We suggest that the mechanism of helix formation may be partly responsible for these observations. In particular, the high negative correlation between residue helical propensities and neighbouring hydrophobicity suggests that hydrophobicity may play a more important role in helix formation than currently recognized.

Folding by numbers: primary sequence statistics and their use in studying protein folding

The exponential growth over the past several decades in the quantity of both primary sequence data available and the number of protein structures determined has provided a wealth of information describing the relationship between protein primary sequence and tertiary structure. This growing repository of data has served as a prime source for statistical analysis, where underlying relationships between patterns of amino acids and protein structure can be uncovered. Here, we survey the main statistical approaches that have been used for identifying patterns within protein sequences, and discuss sequence pattern research as it relates to both secondary and tertiary protein structure. Limitations to statistical analyses are discussed, and a context for their role within the field of protein folding is given. We conclude by describing a novel statistical study of residue patterning in β-strands, which finds that hydrophobic (i,i+2) pairing in β-strands occurs more often than expected at locations near strand termini. Interpretations involving β-sheet nucleation and growth are discussed.

Protein stabilization by the rational design of surface charge-charge interactions

The design of proteins with increased stability has many important applications in biotechnology. In recent years, strategies involving directed evolution, sequence-based design, or computational design have proven successful for generating stabilized proteins. A brief overview of the various methods that have been used to increase protein stability is presented, followed by a detailed example of how the rational design of surface charge-charge interactions has provided a robust method for protein stabilization.

A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions

The design of stable proteins and enzymes is not only of particular biotechnological importance, but also addresses some important fundamental questions. While there are a number of different options available for designing or engineering stable proteins, the field of computational design provides fast and universal methods for stabilizing proteins of interest. One of the successful computational design strategies focuses on stabilizing proteins through the optimization of charge-charge interactions on the protein surface. By optimizing surface interactions, it is possible to alleviate some of the challenges that accompany efforts to redesign the protein core. The rational design of surface charge-charge interactions also allows one to optimize only the interactions that are distant from binding sites or active sites, making it possible to increase stability without adversely affecting activity. The optimization of surface charge-charge interactions is discussed in detail along with the experimental evidence to demonstrate that this is a robust and universal approach to designing proteins with enhanced stability.

Molecular basis for G-actin binding to RPEL motifs from the serum response factor coactivator MAL

Serum response factor transcriptional activity is controlled through interactions with regulatory cofactors such as the coactivator MAL/MRTF-A (myocardin-related transcription factor A). MAL is itself regulated in vivo by changes in cellular actin dynamics, which alter its interaction with G-actin. The G-actin-sensing mechanism of MAL/MRTF-A resides in its N-terminal domain, which consists of three tandem RPEL repeats. We describe the first molecular insights into RPEL function obtained from structures of two independent RPEL^MAL peptide:G-actin complexes. Both RPEL peptides bind to the G-actin hydrophobic cleft and to subdomain 3. These RPEL^MAL:G-actin structures explain the sequence conservation defining the RPEL motif, including the invariant arginine. Characterisation of the RPEL^MAL:G-actin interaction by fluorescence anisotropy and cell reporter-based assays validates the significance of actin-binding residues for proper MAL localisation and regulation in vivo. We identify important differences in G-actin engagement between the two RPEL^MAL structures. Comparison with other actin-binding proteins reveals an unexpected similarity to the vitamin-D-binding protein, extending the G-actin-binding protein repertoire.

Population of On-pathway Intermediates in the Folding of Ubiquitin

The role that intermediate states play in protein folding is the subject of intense investigation and in the case of ubiquitin has been controversial. We present fluorescence-detected kinetic data derived from single and double mixing stopped-flow experiments to show that the F45W mutant of ubiquitin (WT*), a well-studied single-domain protein and most recently regarded as a simple two-state system, folds via on-pathway intermediates. To account for the discrepancy we observe between equilibrium and kinetic stabilities and m-values, we show that the polypeptide chain undergoes rapid collapse to an intermediate whose presence we infer from a fast lag phase in interrupted refolding experiments. Double-jump kinetic experiments identify two direct folding phases that are not associated with slow isomerisation reactions in the unfolded state. These two phases are explained by kinetic partitioning which allows molecules to reach the native state from the collapsed state via two possible competing routes, which we further examine using two destabilised ubiquitin mutants. Interrupted refolding experiments allow us to observe the formation and decay of an intermediate along one of these pathways. A plausible model for the folding pathway of ubiquitin is presented that demonstrates that obligatory intermediates and/or chain collapse are important events in restricting the conformational search for the native state of ubiquitin.

Amino acid substitutions affecting protein dynamics in eglin C do not affect heat capacity change upon unfolding

The heat capacity change upon unfolding (deltaC(p)) is a thermodynamic parameter that defines the temperature dependence of the thermodynamic stability of proteins; however, physical basis of the heat capacity change is not completely understood. Although empirical surface area-based calculations can predict heat capacity changes reasonably well, accumulating evidence suggests that changes in hydration of those surfaces is not the only parameter contributing to the observed heat capacity changes upon unfolding. Because packing density in the protein interior is similar to that observed in organic crystals, we hypothesized that changes in protein dynamics resulting in increased rigidity of the protein structure might contribute to the observed heat capacity change upon unfolding. Using differential scanning calorimetry we characterized the thermodynamic behavior of a serine protease inhibitor eglin C and two eglin C variants with altered native state dynamics, as determined by NMR. We found no evidence of changes in deltaC(p) in either of the variants, suggesting that changes in rigidity do not contribute to the heat capacity change upon unfolding in this model system.

Ubiquitin: a small protein folding paradigm

For the past twenty years, the small, 76-residue protein ubiquitin has been used as a model system to study protein structure, stability, folding and dynamics. In this time, ubiquitin has become a paradigm for both the experimental and computational folding communities. The folding energy landscape is now uniquely characterised with a plethora of information available on not only the native and denatured states, but partially structured states, alternatively folded states and locally unfolded states, in addition to the transition state ensemble. This Perspective focuses on the experimental characterisation of ubiquitin using a comprehensive range of biophysical techniques.

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences

Single amino acid substitutions rarely produce substantial changes in protein structure. Here we show that substitution of the C-cap residue in the alpha-helix of ubiquitin with proline (34P variant) leads to dramatic structural changes. The resulting conformational perturbation extends over the last two turns of the alpha-helix and leads to enhanced flexibility for residues 27-37. Thermodynamic analysis of this ubiquitin variant using differential scanning calorimetry reveals that the thermal unfolding transition remains highly cooperative, exhibiting two-state behavior. Similarities with the wild type in the thermodynamic parameters (heat capacity change upon unfolding and m-value) of unfolding monitored by DSC and chemical denaturation suggests that the 34P variant has comparable buried surface area. The hydrophobic core of 34P variant is not packed as well as that of the wild type protein as manifested by a lower enthalpy of unfolding. The increased mobility of the polypeptide chain of this ubiquitin variant allows the transient opening of the hydrophobic core as evidenced by ANS binding. Taken together, these results suggest exceptional robustness of cooperativity in protein structures.

Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis

The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of this residue in a left-handed conformation or enhanced solvation of the peptide backbone because of the absence of a side chain. Attempts to quantify the contributions of these two effects have been made previously, but the issue remains unresolved. Here we have used chemical protein synthesis to dissect the energetic basis of alpha-helix termination by comparing a series of ubiquitin variants containing an L-amino acid or the corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can adopt a left-handed conformation without energetic penalty, so the contributions of conformational strain and backbone solvation can thus be separated. Analysis of the thermodynamic data revealed that the preference for glycine at the C' position of a helix is predominantly a conformational effect.

Effects of Charge-to-Alanine Substitutions on the Stability of Ribosomal Protein L30e from Thermococcus celer

The ability to rationally engineer a protein with altered stability depends upon the detailed understanding of the role of noncovalent interactions in defining thermodynamic properties of proteins. In this paper, we used T. celer L30e as a model to address the question of the role of charge-charge interactions in defining the stability of this protein. A total of 26 single-site charge-to-alanine variants of this protein were generated, and the stability of these proteins was determined using thermal- and denaturant-induced unfolding. It was found that, although L30e is isolated from a thermophilic organism and is highly thermostable, some of the substitutions lead to a further increase in the transition temperature. Analysis of the effects of high ionic strength on the stabilities of L30e variants shows that the long-range charge-charge interactions are as important as the short-range (salt bridge) interactions. The changes in stabilities of the T. celer L30e protein variants were compared with the changes in the energy of charge-charge interactions calculated using different computational models. It was found that there is a good qualitative agreement between experimental and calculated data: for 70-80% (19-21 of 26, confidence p < 0.003) of the variants, computational models predict correctly the sign of the stability changes. In particular, computational models identify correctly those charged amino acid residue substitutions of which led to enhancement in thermostability. Thus, optimization of the charge-charge interactions might be a useful approach for the rational increase in protein stability.

Ubiquitin folds through a highly polarized transition state

The small alpha/beta protein ubiquitin has been used as a model system for experimental and computational studies on protein folding for many years. Here, we present a comprehensive phi-value analysis and characterize the structure and energetics of the transition state ensemble (TSE). Twenty-seven non-disruptive mutations are made throughout the structure and a range of phi-values from zero to one are observed. The values cluster such that medium and high values and found only in the N-terminal region of the protein, whilst the C-terminal region has consistently low phi-values. In the TSE, the main alpha-helix appears to be fully formed (two phi-values which specifically probe helical structure are one) and the helix is stabilized by packing against the first beta-turn, which is partially structured. In striking comparison, the phi-values in the C-terminal region are all very low, suggesting that this region of the protein is largely unstructured in the TSE. Data are consistent with a nucleation-condensation mechanism in which there is a highly polarized folding nucleus comprising the first beta-hairpin and the alpha-helix. Data presented from the protein engineering study and phi-value analysis are compared with results from other experimental studies and also computational studies.

Extending the folding nucleus of ubiquitin with an independently folding beta-hairpin finger: hurdles to rapid folding arising from the stabilisation of local interactions

The N-terminal beta-hairpin sequence of ubiquitin has been implicated as a folding nucleation site. To extend and stabilise the ubiquitin folding nucleus, we have inserted an autonomously folding 14-residue peptide sequence beta4 which in isolation forms a highly populated beta-hairpin (>70%) stabilised by local interactions. NMR structural analysis of the ubiquitin mutant (Ubeta4) shows that the hairpin finger is fully structured and stabilises ubiquitin by approximately 8kJmol(-1). Protein engineering and kinetic (phi(F)-value) analysis of a series of Ubeta4 mutants shows that the hairpin extension of Ubeta4 is also significantly populated in the transition state (phi(F)-values >0.7) and has the effect of templating the formation of native contacts in the folding nucleus of ubiquitin. However, at low denaturant concentrations the chevron plot of Ubeta4 shows a small deviation from linearity (roll-over effect), indicative of the population of a compact collapsed state, which appears to arise from over-stabilisation of local interactions. Destabilising mutations within the native hairpin sequence and within the engineered hairpin extension, but not elsewhere, eliminate this non-linearity and restore apparent two-state behaviour. The pitfall to stabilising local interactions is to present hurdles to the rapid and efficient folding of small proteins down a smooth folding funnel by trapping partially folded or misfolded states that must unfold or rearrange before refolding.

Thermodynamics Of α‐Helix Formation

The alpha-helix was the first proposed and experimentally confirmed secondary structure. The elegant simplicity of the alpha-helical structure, stabilized by hydrogen bonding between the backbone carbonyl oxygen and the peptide amide four residues away, has captivated the scientific community. In proteins, alpha-helices are also stabilized by the so-called capping interactions that occur at both the C- and the N-termini of the helix. This chapter provides a brief historical overview of the thermodynamic studies of the energetics of helix formation, and reviews recent progress in our understanding of the thermodynamics of helix formation.

Both helical propensity and side-chain hydrophobicity at a partially exposed site in α-helix contribute to the thermodynamic stability of ubiquitin

Improving helical propensity of residues was proposed as one of the approaches to increase protein stability. Here the contribution of the helix propensity and hydrophobicity of residues at partially buried positions of alpha-helix to the stability of a model protein-ubiquitin- is explored. Thermodynamic stabilities of 13 ubiquitin variants with substitutions at a partially buried helical residue were measured by differential scanning calorimetry. It was found that the dynamic range of stabilities for different amino acid residues at this partially buried position is 3 times larger than that expected based on helical propensity alone. Correlation analysis shows that both helical propensity and hydrophobicity are important in defining the relative stabilities of the studied ubiquitin variants. These results provide experimental evidence that partially buried positions are potentially useful sites for engineering proteins with enhanced thermostability.

Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions

Using computational and sequence analysis of bacterial cold shock proteins, we designed a protein (CspB-TB) that has the core residues of mesophilic protein from Bacillus subtilis(CspB-Bs) and altered distribution of surface charged residues. This designed protein was characterized by circular dichroism spectroscopy, and found to have secondary and tertiary structure similar to that of CspB-Bs. The activity of the CspB-TB protein as measured by the affinity to a single-stranded DNA (ssDNA) template at 25 degrees C is somewhat higher than that of CspB-Bs. Furthermore, the decrease in the apparent binding constant to ssDNA upon increase in temperature is much more pronounced for CspB-Bs than for CspB-TB. Temperature-induced unfolding (as monitored by differential scanning calorimetry and circular dichroism spectroscopy) and urea-induced unfolding experiments were used to compare the stabilities of CspB-Bs and CspB-TB. It was found that CspB-TB is approximately 20 degrees C more thermostable than CspB-Bs. The thermostabilization of CspB-TB relative to CspB-Bs is achieved by decrease in the enthalpy and entropy of unfolding without affecting their temperature dependencies, i.e. these proteins have similar heat capacity changes upon unfolding. These changes in the thermodynamic parameters result in the global stability function, i.e. Gibbs energy, deltaG(T), that is shifted to higher temperatures with only small changes in the maximum stability. Such a mechanism of thermostabilization, although predicted from the basic thermodynamic considerations, has never been identified experimentally.

Stability and Folding Kinetics of a Ubiquitin Mutant with a Strong Propensity for Nonnative β-Hairpin Conformation in the Unfolded State

A F45W mutant of yeast ubiquitin has been used as a model system to examine the effects of nonnative local interactions on protein folding and stability. Mutating the native TLTGK G-bulged type I turn in the N-terminal beta-hairpin to NPDG stabilizes a nonnative beta-strand alignment in the isolated peptide fragment. However, NMR structural analysis of the native and mutant proteins shows that the NPDG mutant is forced to adopt the native beta-strand alignment and an unfavorable type I NPDG turn. The mutant is significantly less stable (approximately 9 kJ mol(-1)) and folds 30 times slower than the native sequence, demonstrating that local interactions can modulate protein stability and that attainment of a nativelike beta-hairpin conformation in the transition state ensemble is frustrated by the turn mutations. Surprising, alcoholic cosolvents [5-10% (v/v) TFE] are shown to accelerate the folding rate of the NPDG mutant. We conclude, backed-up by NMR data on the peptide fragments, that even though nonnative states in the denatured ensemble are highly populated and their stability further enhanced in the presence of cosolvents, the simultaneous increase in the proportion of nativelike secondary structure (hairpin or helix), in rapid equilibrium with nonnative states, is sufficient to accelerate the folding process. It is evident that modulating local interactions and increasing nonnative secondary structure propensities can change protein stability and folding kinetics. However, nonlocal contacts formed in the global cooperative folding event appear to determine structural specificity.

Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity

It was established previously that helical propensities of different amino acid residues in the middle of alpha-helix in peptides and in proteins are very similar. The statistical analysis of the protein helices from the known three-dimensional structures shows no difference in the frequency of noncharged residues in the middle and at the C terminus. Yet, experimental studies show distinctive differences for the helical propensities of noncharged residues in the middle and in the C terminus in model peptides. Is this a general effect, and is it applicable to protein helices or is it specific to the model alanine-based peptides? To answer this question, the effects of substitutions at positions 28 (middle residue) and 32 (C2 position at the C terminus) of the alpha-helix of ubiquitin on the stability of this protein are measured by using differential scanning calorimetry. The two data sets produce similar values for intrinsic helix propensity, leading to a conclusion that noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. This conclusion is further supported with an excellent correlation between the helix propensity scale obtained for the two positions in ubiquitin with the experimental helix propensity scale established previously and with the statistical distribution of the residues in protein helices.

Contribution of surface salt bridges to protein stability: guidelines for protein engineering

The small globular protein, ubiquitin, contains a pair of oppositely charged residues, K11 and E34, that according to the three-dimensional structure are located on the surface of this protein with a spatial orientation characteristic of a salt bridge. We investigated the strength of this salt bridge and its contribution to the global stability of the ubiquitin molecule. Using the "double mutant cycle" analysis, the strength of the pairwise interactions between K11 and E34 was estimated to be favorable by 3.6kJ/mol. Further, the salt bridge of the reverse orientation, i.e. E11/K34, can be formed and is found to have a strength (3.8kJ/mol) similar to that of the K11/E34 pair. However, the global stability of the K11/E34 variant of ubiquitin is 2.2kJ/mol higher than that of the E11/K34 variant. The difference in the contribution of the opposing salt bridge orientations to the overall stability of the ubiquitin molecule is attributed to the difference in the charge-charge interactions between residues forming the salt bridge and the rest of the ionizable groups in this protein. On the basis of these results, we concluded that surface salt bridges are stabilizing, but their contribution to the overall protein stability is strongly context-dependent, with charge-charge interactions being the largest determinant. Analysis of 16 salt bridges from six different proteins, for which detailed experimental data on energetics have been reported, support the conclusions made from the analysis of the salt bridge in ubiquitin. Implications of these findings for engineering proteins with enhanced thermostability are discussed.