A simple model for polyproline II structure in unfolded states of alanine-based peptides

Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review

Proline is a unique amino acid in that its side-chain is cyclised to the backbone, thus giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline forms two well-characterized helical structures: a left-handed polyproline helix (PPII) and a right-handed polyproline helix (PPI). Usually, sequences made only of prolyl residues are in PPII conformation, but even sequences not rich in proline but which are rich in glycine, lysine, glutamate, or aspartate have also a tendency to form PPII helices. Currently, the only way to study unambiguously PPII structure in solution is to use spectroscopies based on optical activity such as circular dichroism, vibrational circular dichroism and Raman optical activity. The importance of the PPII structure is emphasized by its ubiquitous presence in different organisms from yeast to human beings where proline-rich motifs and their binding domains are believed to be involved in vital biological processes. Some of the domains that are bound by proline-rich motifs include SH3 domains, WW domains, GYF domains and UEV domains, etc. The PPII structure has been demonstrated to be essential to biological activities such as signal transduction, transcription, cell motility, and immune response.

Electronic Control of Polyproline II Helix Stability via the Identity of Acyl Capping Groups: the Pivaloyl Group Particularly Promotes PPII

The type II polyproline helix (PPII) is a fundamental secondary structure of proteins, important in globular proteins, in intrinsically disordered proteins, and at protein-protein interfaces. PPII is stabilized in part by n→π* interactions between consecutive carbonyls, via electron delocalization between an electron-donor carbonyl lone pair (n) and an electron-acceptor carbonyl (π*) on the subsequent residue. We previously demonstrated that changes to the electronic properties of the acyl donor can predictably modulate the strength of n→π* interactions, with data from model compounds, in solution in chloroform, in the solid state, and computationally. Herein, we examined whether the electronic properties of acyl capping groups could modulate the stability of PPII in peptides in water. In X-PPGY-NH2 peptides (X=10 acyl capping groups), the effect of acyl group identity on PPII was quantified by circular dichroism and NMR spectroscopy. Electron-rich acyl groups promoted PPII relative to the standard acetyl (Ac-) group, with the pivaloyl and iso-butyryl groups most significantly increasing PPII. In contrast, acyl derivatives with electron-withdrawing substituents and the formyl group relatively disfavored PPII. Similar results, though lesser in magnitude, were also observed in X-APPGY-NH2 peptides, indicating that the capping group can impact PPII conformation at both proline and non-proline residues. The pivaloyl group was particularly favorable in promoting PPII. The effects of acyl capping groups were further analyzed in X-DfpPGY-NH2 and X-ADfpPGY-NH2 peptides, Dfp=4,4-difluoroproline. Data on these peptides indicated that acyl groups induced order Piv- > Ac- > For-. These results suggest that greater consideration should be given to the identity of acyl capping groups in inducing structure in peptides.

Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction

Intrinsically disordered proteins (IDPs) adopt a wide array of different conformations that can be constrained by the presence of proline residues, which are frequently found in IDPs. To assess the effects of proline, we designed a series of peptides that differ with respect to the number of prolines in the sequence and their organization. Using high-resolution atomistic molecular dynamics simulations, we found that accounting for whether the proline residues are clustered or isolated contributed significantly to explaining deviations in the experimentally-determined gyration radii of IDPs from the values expected based on the Flory scaling-law. By contrast, total proline content makes smaller contribution to explaining the effect of prolines on IDP conformation. Proline residues exhibit opposing effects depending on their organizational pattern in the IDP sequence. Clustered prolines (i.e., prolines with ≤2 intervening non-proline residues) result in expanded peptide conformations whereas isolated prolines (i.e., prolines with >2 intervening non-proline residues) impose compacted conformations. Clustered prolines were estimated to induce an expansion of ∼20% in IDP dimension (via formation of PPII structural elements) whereas isolated prolines were estimated to induce a compaction of ∼10% in IDP dimension (via the formation of backbone turns). This dual role of prolines provides a mechanism for conformational switching that does not rely on the kinetically much slower isomerization of cis proline to the trans form. Bioinformatic analysis demonstrates high populations of both isolated and clustered prolines and implementing them in coarse-grained molecular dynamics models illustrates that they improve the characterization of the conformational ensembles of IDPs.

Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water

The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar trapezoid that is not much larger than the size of water molecules. When the finite size of a water molecule is considered, the stabilization from solvent polarization for such a trapezoid is frustrated. Water molecules cannot find orientations to properly stabilize all four polar regions close to each other with such an awkward arrangement. This leads to quite substantial reduction in polarization stabilization. Although the polyproline II (PP-II) conformation is very similar to the β strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization, when combined with favorable intrapeptide interactions, leads to the PP-II to be lowest in free energy. Other factors, such as the entropic TΔS and the ϕ, ψ coupling terms, are also studied but are found to play only a minor role. The insight shown in this work helps to better understand the structure of globular and intrinsic disordered proteins and facilitate future force field development.

Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix

n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe₂, Ac-Ala-NMe₂, and Ac-Pro₂-NMe₂. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.

Reframing the Protein Folding Problem: Entropy as Organizer

It has been a long-standing conviction that a protein's native fold is selected from a vast number of conformers by the optimal constellation of enthalpically favorable interactions. In marked contrast, this Perspective introduces a different mechanism, one that emphasizes conformational entropy as the principal organizer in protein folding while proposing that the conventional view is incomplete. This mechanism stems from the realization that hydrogen bond satisfaction is a thermodynamic necessity. In particular, a backbone hydrogen bond may add little to the stability of the native state, but a completely unsatisfied backbone hydrogen bond would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization, typically between -5 and -15 kcal/mol under physiological conditions. Consequently, upon folding, buried backbone polar groups must form hydrogen bonds, and they do so by assembling scaffolds of α-helices and/or strands of β-sheet, the only conformers in which, with rare exception, hydrogen bond donors and acceptors are exactly balanced. In addition, only a few thousand viable scaffold topologies are possible for a typical protein domain. This thermodynamic imperative winnows the folding population by culling conformers with unsatisfied hydrogen bonds, thereby reducing the entropy cost of folding. Importantly, conformational restrictions imposed by backbone···backbone hydrogen bonding in the scaffold are sequence-independent, enabling mutation─and thus evolution─without sacrificing the structure.

AlphaFold and Implications for Intrinsically Disordered Proteins

Accurate predictions of the three-dimensional structures of proteins from their amino acid sequences have come of age. AlphaFold, a deep learning-based approach to protein structure prediction, shows remarkable success in independent assessments of prediction accuracy. A significant epoch in structural bioinformatics was the structural annotation of over 98% of protein sequences in the human proteome. Interestingly, many predictions feature regions of very low confidence, and these regions largely overlap with intrinsically disordered regions (IDRs). That over 30% of regions within the proteome are disordered is congruent with estimates that have been made over the past two decades, as intense efforts have been undertaken to generalize the structure-function paradigm to include the importance of conformational heterogeneity and dynamics. With structural annotations from AlphaFold in hand, there is the temptation to draw inferences regarding the "structures" of IDRs and their interactomes. Here, we offer a cautionary note regarding the misinterpretations that might ensue and highlight efforts that provide concrete understanding of sequence-ensemble-function relationships of IDRs. This perspective is intended to emphasize the importance of IDRs in sequence-function relationships (SERs) and to highlight how one might go about extracting quantitative SERs to make sense of how IDRs function.

Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins

The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.

Development of fructose-1,6-bisphosphate aldolase enzyme peptide mimics as biocatalysts in direct asymmetric aldol reactions

This study describes the design and synthesis of mimetic peptides modelled on the catalytic active site of the fructose-1,6-bisphosphate aldolase (FBPA) enzyme. The synthesized peptides consisting of the turn motifs and catalytic site amino acids of FBPA enzyme were evaluated for catalytic activity in direct asymmetric aldol reactions of ketones and aldehydes. The influence of substrate scope, catalyst loading and solvents including water, on the reaction were also investigated. Nuclear magnetic resonance (NMR) and circular dichroism (CD) were used to determine the secondary structure of the peptides to provide an understanding of the structure–activity relationship. The peptides showed catalytic activity and the aldol products were obtained in low yields (up to 44%), but excellent enantioselectivity (up to 93%) and moderate diastereoselectivity (65 : 35).

Novel asymmetric aldol reaction catalysing fructose-1,6-bisphosphate aldolase peptide mimics with secondary structural motifs.

The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators

Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable three-dimensional structure, but rather adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. In IDPs, proline residues are significantly enriched. Given their unique physicochemical and structural properties, a more detailed understanding of their potential role in stabilizing partially folded states in IDPs is highly desirable. Nuclear magnetic resonance (NMR) spectroscopy, and in particular ¹³C-detected NMR, is especially suitable to address these questions. We applied a ¹³C-detected strategy to study Osteopontin, a largely disordered IDP with a central compact region. By using the exquisite sensitivity and spectral resolution of these novel techniques, we gained unprecedented insight into cis-Pro populations, their local structural dynamics, and their role in mediating long-range contacts. Our findings clearly call for a reassessment of the structural and functional role of proline residues in IDPs. The emerging picture shows that proline residues have ambivalent structural roles. They are not simply disorder promoters but rather can, depending on the primary sequence context, act as nucleation sites for structural compaction in IDPs. These unexpected features provide a versatile mechanistic toolbox to enrich the conformational ensembles of IDPs with specific features for adapting to changing molecular and cellular environments.

Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias

Conformational equilibria in the protein denatured state have key roles regulating folding, stability, and function. The extent of conformational bias in the protein denatured state under folding conditions, however, has thus far proven elusive to quantify, particularly with regard to its sequence dependence and energetic character. To better understand the structural preferences of the denatured state, we analyzed both the sequence dependence to the mean hydrodynamic size of disordered proteins in water and the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the α and polyproline II (PPII) backbone conformations can be obtained. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the protein reveal amino acid specific preferences for PPII that are in good quantitative agreement with calorimetry-measured values from unfolded peptides and those inferred by survey of the protein coil library. At temperatures above 25 °C, the denatured state follows the predictions of a PPII-dominant ensemble. Heat effects on coil hydrodynamic size indicate the α bias is comparable to the PPII bias at cold temperatures. Though historically thought to give poor resolution to structural details, the hydrodynamic size of the unfolded state is found to be an effective reporter on the extent of the biases for the α and PPII backbone conformations.

Delineation of a new structural motif involving NHN γ-turn

Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal C^α ···C^α distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.

Stimuli-Responsive, Pentapeptide, Nanofiber Hydrogel for Tissue Engineering

Short peptides are uniquely versatile building blocks for self-assembly. Supramolecular peptide assemblies can be used to construct functional hydrogel biomaterials-an attractive approach for neural tissue engineering. Here, we report a new class of short, five-residue peptides that form hydrogels with nanofiber structures. Using rheology and spectroscopy, we describe how sequence variations, pH, and peptide concentration alter the mechanical properties of our pentapeptide hydrogels. We find that this class of seven unmodified peptides forms robust hydrogels from 0.2-20 kPa at low weight percent (less than 3 wt %) in cell culture media and undergoes shear-thinning and rapid self-healing. The peptides self-assemble into long fibrils with sequence-dependent fibrillar morphologies. These fibrils exhibit a unique twisted ribbon shape, as visualized by transmission electron microscopy (TEM) and Cryo-EM imaging, with diameters in the low tens of nanometers and periodicities similar to amyloid fibrils. Experimental gelation behavior corroborates our molecular dynamics simulations, which demonstrate peptide assembly behavior, an increase in β-sheet content, and patterns of variation in solvent accessibility. Our rapidly assembling pentapeptides for injectable delivery (RAPID) hydrogels are syringe-injectable and support cytocompatible encapsulation of oligodendrocyte progenitor cells (OPCs), as well as their proliferation and three-dimensional process extension. Furthermore, RAPID gels protect OPCs from mechanical membrane disruption and acute loss of viability when ejected from a syringe needle, highlighting the protective capability of the hydrogel as potential cell carriers for transplantation therapies. The tunable mechanical and structural properties of these supramolecular assemblies are shown to be permissive to cell expansion and remodeling, making this hydrogel system suitable as an injectable material for cell delivery and tissue engineering applications.

Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids

Experimentally derived, amino acid specific backbone dihedral angle distributions are invaluable for modeling data-driven conformational equilibria of proteins and for enabling quantitative assessments of the accuracies of molecular mechanics force fields. The protein coil library that is extracted from analysis of high-resolution structures of proteins has served as a useful proxy for quantifying intrinsic and context-dependent conformational distributions of amino acids. However, data that go into coil libraries will have hidden biases, and ad hoc procedures must be used to remove these biases. Here, we combine high-resolution biased information from protein structural databases with unbiased low-resolution information from spectroscopic measurements of blocked amino acids to obtain experimentally derived and computationally optimized coil-library landscapes for each of the 20 naturally occurring amino acids. Quantitative descriptions of conformational distributions require parsing of data into conformational basins with defined envelopes, centers, and statistical weights. We develop and deploy a numerical method to extract conformational basins. The weights of conformational basins are optimized to reproduce quantitative inferences drawn from spectroscopic experiments for blocked amino acids. The optimized distributions serve as touchstones for assessments of intrinsic conformational preferences and for quantitative comparisons of molecular mechanics force fields.

Probing the functional conformations of an atypical proline-rich fusion peptide

Simulations confirm a propensity for extended and solvent exposed conformations of the p15 fusion peptide capable of membrane targeting.

The polypeptide biophysics of proline/alanine-rich sequences (PAS): Recombinant biopolymers with PEG-like properties

PAS polypeptides comprise long repetitive sequences of the small L‐amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half‐life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL‐1Ra. Data from size exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy and quantification of hydrodynamic and polar properties demonstrate that the biosynthetic PAS polypeptides exhibit random coil behavior in aqueous solution astonishingly similar to the chemical polymer poly‐ethylene glycol (PEG). The solvent‐exposed PAS peptide groups, in the absence of secondary structure, account for strong hydrophilicity, with negligible contribution by the Ser side chains. Notably, PAS polypeptides exceed PEG of comparable molecular mass in hydrophilicity and hydrodynamic volume while exhibiting lower viscosity. Their uniform monodisperse composition as genetically encoded polymers and their biological nature, offering biodegradability, render PAS polypeptides a promising PEG mimetic for biopharmaceutical applications.

Construction and comparison of the statistical coil states of unfolded and intrinsically disordered proteins from nearest-neighbor corrected conformational propensities of short peptides

Assessing the influence of nearest neighbors on the conformational ensemble of amino acid residues in unfolded and intrinsically disordered proteins and peptides is pivotal for a thorough understanding of the statistical coil state of unfolded proteins as well as of the energetics of the folding process. Research aimed at exploring nearest neighbor interactions has mostly focused on the analysis of restricted coil libraries that reflect conformational distributions in loops connecting more regular secondary structure segments. Recently, however, Toal et al. reported an experimentally based structural analysis of selected xy-pairs in GxyG tetrapeptides, which revealed quantitative information about conformational changes induced by nearest-neighbor interactions (Eur. J. Chem., 2015, 21, 5173-5192). Here, we perform analyses of Ramachandran plots of xy-pairs in GxyG and in coil libraries (Ting et al., PLOS CompBiol, 2010, 6, e1000763) using Hellinger distances as a quantitative measure of dissimilarities between Ramachandran distributions. Our analysis reveals that nearest-neighbor effects inferred from the above coil library are much less pronounced than corresponding structural changes observed for GxyG peptides. To determine whether nearest-neighbor induced conformational changes observed for GxyG can be utilized for the analysis of unfolded proteins, we analyzed sets of ³J(H^HH^α) coupling constants of three different unfolded proteins, namely the 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein (FnBPc), denatured hen lysozyme, and the htau40 protein. For the first two proteins we found statistically meaningful correlations between predicted nearest-neighbor induced changes of ³J(H^HH^α) and experimentally observed deviations from corresponding coupling constants of GxG peptides in water, which we used as reference system with minimal nearest-neighbor interactions. This observation is in line with the NMR based understanding of these proteins being predominantly statistical coils. For htau40, however, which is known to exhibit residual structure and large deviations form statistical coil expectations, these correlations are weak or absent. Our results thus underscore the importance of nearest-neighbor interactions for a complete physical description of an ideal statistical coil state of a protein.

Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H₂ O, Ala₂ H⁺ ⋅18 H₂ O, and Ala₂ ⋅18 H₂ O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.

Human Antimicrobial Peptides in Bodily Fluids: Current Knowledge and Therapeutic Perspectives in the Postantibiotic Era

Antimicrobial peptides (AMPs) are an integral part of the innate immune defense mechanism of many organisms. Due to the alarming increase of resistance to antimicrobial therapeutics, a growing interest in alternative antimicrobial agents has led to the exploitation of AMPs, both synthetic and isolated from natural sources. Thus, many peptide-based drugs have been the focus of increasing attention by many researchers not only in identifying novel AMPs, but in defining mechanisms of antimicrobial peptide activity as well. Herein, we review the available strategies for the identification of AMPs in human body fluids and their mechanism(s) of action. In addition, an overview of the distribution of AMPs across different human body fluids is provided, as well as its relation with microorganisms and infectious conditions.

Self-assembly and sequence length dependence on nanofibrils of polyglutamine peptides

Huntington's disease (HD) is recognized as a currently incurable, inherited neurodegenerative disorder caused by the accumulation of misfolded polyglutamine (polyQ) peptide aggregates in neuronal cells. Yet, the mechanism by which newly formed polyQ chains interact and assemble into toxic oligomeric structures remains a critical, unresolved issue. In order to shed further light on the matter, our group elected to investigate the folding of polyQ peptides - examining glutamine repeat lengths ranging from 3 to 44 residues. To characterize these aggregates we employed a diverse array of technologies, including: nuclear magnetic resonance; circular dichroism; Fourier transform infrared spectroscopy; fluorescence resonance energy transfer (FRET), and atomic force microscopy. The data we obtained suggest that an increase in the number of glutamine repeats above 14 residues results in disordered loop structures, with different repeat lengths demonstrating unique folding characteristics. This differential folding manifests in the formation of distinct nano-sized fibrils, and on this basis, we postulate the idea of 14 polyQ repeats representing a critical loop length for neurotoxicity - a property that we hope may prove amenable to future therapeutic intervention. Furthermore, FRET measurements on aged assemblages indicate an increase in the end-to-end distance of the peptide with time, most probably due to the intermixing of individual peptide strands within the nanofibril. Further insight into this apparent time-dependent reorganization of aggregated polyQ peptides may influence future disease modeling of polyQ-related proteinopathies, in addition to directing novel clinical innovations.

IMPIPS: the immune protection-inducing protein structure concept in the search for steric-electron and topochemical principles for complete fully-protective chemically synthesised vaccine development

Determining immune protection-inducing protein structures (IMPIPS) involves defining the stereo-electron and topochemical characteristics which are essential in MHC-p-TCR complex formation. Modified high activity binding peptides (mHABP) were thus synthesised to produce a large panel of IMPIPS measuring 26.5 ±3.5Å between the farthest atoms fitting into Pockets 1 to 9 of HLA-DRβ1* structures. They displayed a polyproline II-like (PPII_L) structure with their backbone O and N atoms orientated to establish H-bonds with specific residues from HLA-DRβ1*-peptide binding regions (PBR). Residues having specific charge and gauche⁺ orientation regarding p3χ1, p5χ2, and p7χ1 angles determined appropriate rotamer orientation for perfectly fitting into the TCR to induce an appropriate immune response. Immunological assays in Aotus monkeys involving IMPIPS mixtures led to promising results; taken together with the aforementioned physicochemical principles, non-interfering, long-lasting, protection-inducing, multi-epitope, multistage, minimal subunit-based chemically-synthesised peptides can be designed against diseases scourging humankind.

Predictive atomic resolution descriptions of intrinsically disordered hTau40 and α-synuclein in solution from NMR and small angle scattering

The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and α-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation.

Conformational analysis of Gly-Ala-NHMe in D(2)O and DMSO solutions: a two-dimensional infrared spectroscopy study

A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy. The pump-probe scheme with ultrashort mid-infrared pulses, in the Amide I region, is used to determine the mutual orientation of the two C═O bonds and the dynamics due to solute-solvent interactions. The coupling between Amide I modes is evaluated from both linear and 2D spectra. The interconversion between the different conformations occurs on time scales longer than the vibrational lifetime, and the spectral diffusion observed in 2D spectra is attributed to the solvent dynamics. Quantum mechanical calculations and molecular dynamics simulations are performed to identify the most stable geometries. By comparing the experimental and the theoretical data, we establish the prevalence of β-like polar conformers in both water and DMSO solvents.

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

The local conformational (φ, ψ, χ) preferences of amino acid residues remain an active research area, which are important for the development of protein force fields. In this perspective article, we first summarize spectroscopic studies of alanine-based short peptides in aqueous solution. While most studies indicate a preference for the P(II) conformation in the unfolded state over α and β conformations, significant variations are also observed. A statistical analysis from various coil libraries of high-resolution protein structures is then summarized, which gives a more coherent view of the local conformational features. The φ, ψ, χ distributions of the 20 amino acids have been obtained from a protein coil library, considering both backbone and side-chain conformational preferences. The intrinsic side-chain χ(1) rotamer preference and χ(1)-dependent Ramachandran plot can be generally understood by combining the interaction of the side-chain Cγ/Oγ atom with two neighboring backbone peptide groups. Current all-atom force fields such as AMBER ff99sb-ILDN, ff03 and OPLS-AA/L do not reproduce these distributions well. A method has been developed by combining the φ, ψ plot of alanine with the influence of side-chain χ(1) rotamers to derive the local conformational features of various amino acids. It has been further applied to improve the OPLS-AA force field. The modified force field (OPLS-AA/C) reproduces experimental (3)J coupling constants for various short peptides quite well. It also better reproduces the temperature-dependence of the helix-coil transition for alanine-based peptides. The new force field can fold a series of peptides and proteins with various secondary structures to their experimental structures. MD simulations of several globular proteins using the improved force field give significantly less deviation (RMSD) to experimental structures. The results indicate that the local conformational features from coil libraries are valuable for the development of balanced protein force fields.

The high immunogenicity induced by modified sporozoites' malarial peptides depends on their phi (ϕ) and psi (ψ) angles

The importance of CSP- and STARP-derived ϕ and ψ dihedral angles in mHABP structure was analysed by (1)H NMR in the search for molecules which can be included as components of a first-line-of-defence Plasmodium falciparum sporozoite multi-epitope vaccine against the most lethal form of human malaria. Most of the aforementioned dihedral angles were left-hand-like polyproline type II (PPII(L)) structures whilst others had right-hand-like α-helix (α(R)), thus allowing mHABPS to fit better into MHCII molecules and thereby form an appropriate pMHCII complex and also establish the H-bonds which stabilise such complex and by this means induce an appropriate immune response. This information has great implications for vaccine development, malaria being one of them.

Reducing the dimensionality of the protein-folding search problem

How does a folding protein negotiate a vast, featureless conformational landscape and adopt its native structure in biological real time? Motivated by this search problem, we developed a novel algorithm to compare protein structures. Procedures to identify structural analogs are typically conducted in three-dimensional space: the tertiary structure of a target protein is matched against each candidate in a database of structures, and goodness of fit is evaluated by a distance-based measure, such as the root-mean-square distance between target and candidate. This is an expensive approach because three-dimensional space is complex. Here, we transform the problem into a simpler one-dimensional procedure. Specifically, we identify and label the 11 most populated residue basins in a database of high-resolution protein structures. Using this 11-letter alphabet, any protein's three-dimensional structure can be transformed into a one-dimensional string by mapping each residue onto its corresponding basin. Similarity between the resultant basin strings can then be evaluated by conventional sequence-based comparison. The disorder → order folding transition is abridged on both sides. At the onset, folding conditions necessitate formation of hydrogen-bonded scaffold elements on which proteins are assembled, severely restricting the magnitude of accessible conformational space. Near the end, chain topology is established prior to emergence of the close-packed native state. At this latter stage of folding, the chain remains molten, and residues populate natural basins that are approximated by the 11 basins derived here. In essence, our algorithm reduces the protein-folding search problem to mapping the amino acid sequence onto a restricted basin string.

Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out (1)H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked amino-acids (Ac-X-NHMe), oligopeptides (Ac-GGXGG-NH(2)), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.

Assignment of PolyProline II conformation and analysis of sequence--structure relationship

BACKGROUND

Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions.

METHODOLOGY/PRINCIPAL FINDINGS

A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined.

CONCLUSIONS/SIGNIFICANCE

The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.

Spider silk: understanding the structure-function relationship of a natural fiber

Spider silk is of great interest because of its extraordinary physical properties, such as strength and toughness. Here we discuss how these physical properties relate to the way in which spiders have utilized this material in prey capture, forcing its evolution to a high-performance fiber. Female spiders can produce up to seven different types of silk, and all these have different physical properties, which relate to their various functions. The variation in properties are due to underlying differences in the proteins making up these silks. As our understanding of spider silk has increased in the recent years, it has been possible to produce recombinant versions of the respective proteins. Recombinant proteins open up the potential to produce synthetic silk fibers with properties similar to those of the natural spider silk threads.

Physical-chemical determinants of coil conformations in globular proteins

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from alpha-helices and/or beta-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray-elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical-chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue.

The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures

It has been suggested that denatured proteins are predisposed toward the left-handed polyproline II (P(II)) conformation. One possible source of P(II) stability in the denatured state is water bridges. Water bridges are networks of water molecules that link nearby hydrogen bond acceptors and/or donors on proteins. On the basis of the proposed behavior of P(II) and water bridges, the propensity of a residue to participate in water bridges should be correlated with its P(II) propensity. To test this hypothesis, we analyzed the following data sets: 2351 high-resolution crystal structures, and the native and denatured states of 188 different proteins from all-atom, explicit-solvent molecular dynamics (MD) simulations, which are part of our Dynameomics effort. We found that water bridges do not explain the high frequency of P(II) in denatured states; such bridges are less frequent around P(II) than around other conformations. Thus, this analysis casts doubt on water bridges as a dominant factor determining the residue-based P(II) propensities.

Salt dependence of an alpha-helical peptide folding energy landscapes

We used CD, UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Psi angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine alpha-helical peptide, AP of sequence AAAAA(AAARA)(3)A. NaClO(4) stabilizes alpha-helical-like conformations more than does NaCl, which stabilizes more than Na(2)SO(4) at identical ionic strengths. This alpha-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding. Much of the NaClO(4) alpha-helix stabilization results from ClO(4)(-) association with the AP terminal -NH(3)(+) groups and Arg side chains. ClO(4)(-) stabilizes 3(10)-helix conformations but destabilizes turn conformations. The decreased Cl(-) and SO(4)(2-) AP alpha-helix stabilization probably results from a decreased association with the Arg and terminal -NH(3)(+) groups. Cl(-) is expected to have a smaller binding affinity and thus stabilizes alpha-helical conformations intermediately between NaClO(4) and Na(2)SO(4). Electrostatic screening stabilizes pi-bulge conformations.

Multivalency in the assembly of intrinsically disordered Dynein intermediate chain

Dynein light chains are thought to increase binding efficiency of dynein intermediate chain to both dynein heavy chain and dynactin, but their exact role is not clear. Isothermal titration calorimetry and x-ray crystallography reported herein indicate that multivalency effects underlie efficient dynein assembly and regulation. For a ternary complex of a 60-amino acid segment of dynein intermediate chain (IC) bound to two homodimeric dynein light chains Tctex1 and LC8, there is a 50-fold affinity enhancement for the second light chain binding. For a designed IC construct containing two LC8 sites, observed the 1000-fold enhancement reflects a remarkably pure entropic chelate effect of a magnitude commensurate with theoretical predictions. The lower enhancement in wild-type IC is attributed to unfavorable free energy changes associated with incremental interactions of IC with Tctex1. Our results show assembled dynein IC as an elongated, flexible polybivalent duplex, and suggest that polybivalency is an important general mechanism for constructing stable yet reversible and functionally versatile complexes.

Polar or apolar--the role of polarity for urea-induced protein denaturation

Urea-induced protein denaturation is widely used to study protein folding and stability; however, the molecular mechanism and driving forces of this process are not yet fully understood. In particular, it is unclear whether either hydrophobic or polar interactions between urea molecules and residues at the protein surface drive denaturation. To address this question, here, many molecular dynamics simulations totalling ca. 7 µs of the CI2 protein in aqueous solution served to perform a computational thought experiment, in which we varied the polarity of urea. For apolar driving forces, hypopolar urea should show increased denaturation power; for polar driving forces, hyperpolar urea should be the stronger denaturant. Indeed, protein unfolding was observed in all simulations with decreased urea polarity. Hyperpolar urea, in contrast, turned out to stabilize the native state. Moreover, the differential interaction preferences between urea and the 20 amino acids turned out to be enhanced for hypopolar urea and suppressed (or even inverted) for hyperpolar urea. These results strongly suggest that apolar urea–protein interactions, and not polar interactions, are the dominant driving force for denaturation. Further, the observed interactions provide a detailed picture of the underlying molecular driving forces. Our simulations finally allowed characterization of CI2 unfolding pathways. Unfolding proceeds sequentially with alternating loss of secondary or tertiary structure. After the transition state, unfolding pathways show large structural heterogeneity.

To perform their physiological function, proteins have to fold into their characteristic three-dimensional structure. While the folded state is stable under physiological conditions, changes in the solvent can destabilize the folded state and even induce denaturation. One of the most commonly used denaturants is urea. Despite its widespread use to study protein folding and stability, however, the molecular mechanism and particularly the driving forces of urea-induced protein denaturation are not yet understood. Two mechanisms have been suggested, according to which denaturation is driven either by polar interactions via hydrogen bonds or by hydrophobic interactions with apolar amino acids. By systematically varying urea polarity and quantifying the interactions of the solvent molecules with all amino acids of the protein, the present simulation study reveals that it is mainly the apolar interactions that drive denaturation. Our results suggest a coherent microscopic picture for urea-induced denaturation and bear more general implications for protein stability in other environments, e.g., in chaperone-assisted folding.

Is There or Isn't There? The Case for (and Against) Residual Structure in Chemically Denatured Proteins

First raised some 60 years ago, the question of whether chemically denatured proteins are fully unfolded has, in recent years, seen significantly renewed interest. This increased attention has been spurred, in large part, by new spectroscopic and computational approaches that suggest even the most highly denatured polypeptides contain significant residual structure. In contrast, the most recent scattering results uphold the long-standing view that chemically denatured proteins adopt random coil configurations. Here we review the evidence both for and against residual structure in chemically denatured proteins, and attempt to reconcile these seemingly contradictory observations.

Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain

The left-handed polyproline II helical structure (P(II)) is observed to be a dominant conformation in the disordered states of protein and small polypeptide chains, even when no prolines are present in the sequence. Recently, in work by Ferreon and Hilser, the energetics associated with Ala and Gly substitutions at a surface exposed proline site were determined calorimetrically by measuring the binding energetics of Sos peptide variants to the C-terminal Src Homology 3 domain of SEM-5. The results were interpreted as a significant conformational bias toward the bound conformation (i.e., P(II)), even when the ligand is unbound. That study was not able to determine, however, whether the conformational bias of the peptides could be explained in terms other than that of a P(II) preference. Here, we test, using a computer algorithm based on the hard sphere collision (HSC) model, the notion of whether a bias in the unbound states of the peptide ligands is specific for the P(II) conformation, or if a bias to any other region of (phi, psi) space can also result in the same observed binding energetics. The results of these computer simulations indicate that, of the regions of (phi, psi) modeled for bias in the small peptides, only the bias to the P(II) conformation, and at rates of bias similar to the experimentally observed rates, quantitatively reproduced the experimental binding energetics.

Conformational and orientational transformation of silk proteins in the major ampullate gland of Nephila clavipes spiders

The orientational and conformational transformation of the native liquid silk into a solid fiber in the major ampullate gland of the spider Nephila clavipes has been studied by Raman spectromicroscopy. The spectra show that the conformation of silk proteins in the glandular sac contains several secondary structure elements, which is consistent with intrinsically unfolded proteins. A few alpha-helices are also present and involve some alanine residues located in the polyalanine segments of the spidroin sequence. The conversion of the silk solution in the major ampullate gland appears to be a two-state process without intermediate states. In the first and second limbs of the duct, silk is isotropic and spidroins are generally native-like. beta-Sheets start to develop between the second and the third limb of the duct, suggesting that early beta-sheets are generated by shear forces. However, most of the beta-sheets are formed between the draw down taper and the valve. The early beta-sheets formed upward of the draw down taper might play the role of nucleation sites for the subsequent beta-sheet aggregation. The alignment of the polypeptides chains occurs near the valve, revealing that orientational and conformational changes do not occur simultaneously. Extensional flow seems to be the driving force to produce the orientational order, which in turn is associated with the formation of the major part of the beta-sheets. The slow evolution of the spidroin conformation up to the draw down taper followed by the rapid transformation between the drawn down taper and the valve may be important to achieve the optimal structure of the final fiber.

LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana

BACKGROUND

LEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown.

RESULTS

We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded.

CONCLUSION

The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins.

LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana

Background

LEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown.

Results

We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded.

Conclusion

The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins.