Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution

Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes

A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK)5, (EKKE)5, (ERER)5, (ERRE)5, and (EKER)5. The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE)5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE)5, as well as the sequences with the equivalent amino acid content, (ERER)5, exhibited no aggregate formation under equivalent pH and concentration conditions.

Autosomal recessive variants c.953A>C and c.97-1G>C in NSUN2 causing intellectual disability: a molecular dynamics simulation study of loss-of-function mechanisms

Introduction

Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70.

Methods

The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants.

Results and discussion

Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A>C; p.Tyr318Ser in exon-9 of the NSUN2. The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as "SAM-dependent methyltransferase RsmB/NOP2-type". Whereas in family B, we identified a novel splice site variant c.97-1G>C that affects the splice acceptor site of NSUN2. The identified splice variant (c.97-1G>C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs^*16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population.

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.

Sequence-Controlled Secondary Structures and Stimuli Responsiveness of Bioinspired Polyampholytes

A comprehensive study focusing on the influence of the sequence charge pattern on the secondary structure preferences of annealed polyampholytes and their responsiveness to external stimuli is presented. Two sequences are designed composed entirely of ionizable amino acids (charge fraction, f = 1) and an equal number of positive and negative charges (f+ = f- = 0.5) with distinct charge patterns consisting of lysine and glutamic acid monomers. The study reveals that the sequence charge pattern has a significant influence on the secondary structure preferences of polyampholytes at physiological pH. Furthermore, it shows that external stimuli such as pH, ionic strength, and solvent dielectric constant can be used to modulate the secondary structure of the two studied sequences. The observed secondary structure transformations for the two sequences are also substantially different from those determined for uniformly charged homo-polypeptides under matching conditions.

Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields

The potentials of mean force (PMFs) along the end‐to‐end distance of two different helical peptides have been obtained and benchmarked using the adaptive steered molecular dynamics (ASMD) method. The results depend strongly on the choice of force field driving the underlying all‐atom molecular dynamics, and are reported with respect to the three most popular CHARMM force field versions: c22, c27 and c36. Two small peptides, ALA10 and 1PEF, serve as the particular case studies. The comparisons between the versions of the CHARMM force fields provides both a qualitative and quantitative look at their performance in forced unfolding simulations in which peptides undergo large changes in structural conformations. We find that ASMD with the underlying c36 force field provides the most robust results for the selected benchmark peptides.

Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase

Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4–7.6 ​kJ/mol increase in the activation energy of thermal inactivation at 63 ​°C. High resolution X-ray crystal structures (1.15–1.80 ​Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 ​Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.

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Random mutagenesis yields a 15-fold increase in nitrile hydratase thermostability.

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Salt bridges and hydrogen bonds improves nitrile hydratase thermostability.

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Water-mediated hydrogen bonds improves protein thermostability.

Variants in ATP6V0A1 cause progressive myoclonus epilepsy and developmental and epileptic encephalopathy

The vacuolar H+-ATPase is a large multi-subunit proton pump, composed of an integral membrane V0 domain, involved in proton translocation, and a peripheral V1 domain, catalysing ATP hydrolysis. This complex is widely distributed on the membrane of various subcellular organelles, such as endosomes and lysosomes, and plays a critical role in cellular processes ranging from autophagy to protein trafficking and endocytosis. Variants in ATP6V0A1, the brain-enriched isoform in the V0 domain, have been recently associated with developmental delay and epilepsy in four individuals. Here, we identified 17 individuals from 14 unrelated families with both with new and previously characterized variants in this gene, representing the largest cohort to date. Five affected subjects with biallelic variants in this gene presented with a phenotype of early-onset progressive myoclonus epilepsy with ataxia, while 12 individuals carried de novo missense variants and showed severe developmental and epileptic encephalopathy. The R740Q mutation, which alone accounts for almost 50% of the mutations identified among our cases, leads to failure of lysosomal hydrolysis by directly impairing acidification of the endolysosomal compartment, causing autophagic dysfunction and severe developmental defect in Caenorhabditis elegans. Altogether, our findings further expand the neurological phenotype associated with variants in this gene and provide a direct link with endolysosomal acidification in the pathophysiology of ATP6V0A1-related conditions.

Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics

The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, respectively, in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)kF-NH2 and a natural α-helical peptide a2N (1-17) provide evidence of the hypothesis's generality. Adaptive steered molecular dynamics was employed to investigate the mechanical unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramolecular backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mechanical unfolding of the α-helical peptides results in a turnover mechanism in which a 310-helical structure forms during the unfolding, remaining at a near constant population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the average force required to pull alanine-rich α-helical peptides in between the endpoints-namely the native structure and free coil-is nearly independent of the length or the specific primary structure.

Collective excitations in α-helical protein structures interacting with the water environment

Low-frequency vibrational excitations of protein macromolecules in the terahertz frequency region are suggested to contribute to many biological processes such as enzymatic catalysis, intra-protein energy/charge transport, recognition, and allostery. To explain high effectiveness of these processes, two possible mechanisms of the long-lived excitation were proposed by H. Fröhlich and A.S. Davydov, which relate to either vibrational modes or solitary waves, respectively. In this paper, we developed a quantum dynamic model of vibrational excitation in α-helical proteins interacting with the aqueous environment. In the model, we distinguished three coupled subsystems, i.e., (i) a chain of hydrogen-bonded peptide groups (PGs), interacting with (ii) the subsystem of the side-chain residuals which in turn interact with (iii) the environment, surrounding water responsible for dissipation and fluctuation in the system. It was shown that the equation of motion for phonon variables of the PG chain can be transformed to nonlinear Schrodinger equation which admits bifurcation into the solution corresponding to the weak-damped vibrational modes (Fröhlich-type regime) and Davydov solitons. A bifurcation parameter is derived through the strength of phonon-phonon interaction between the side-chains and hydration-shell water molecules. As shown, the energy of these excited states is pumped through the interaction of the side-chains with fluctuating water environment of the proteins. The suggested mechanism of the collective vibrational mode excitation is discussed in connection with the recent experiments on the long-lived collective protein excitations in the terahertz frequency region and vibrational energy transport pathways in proteins.

The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective

Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO₂, SO₂ and NO₂ that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ₄₂ peptide due to its interaction of toxic gas (CO, CO₂, SO₂ and NO₂). During the 400 ns simulation, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes have smaller Root Mean Square Deviation values when compared to the Aβ₄₂ peptide, which shows that the interaction of toxic gases (CO, CO₂, SO_2, and NO₂) would increase the Aβ₄₂ peptide structural stability. The radius of gyration analysis also supports that Aβ₄₂ interacted CO₂ and SO₂ complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ₄₂ interacted CO₂ and SO₂ complexes have a greater compact structure in comparison to Aβ₄₂ interacted CO and NO₂ complexes. Furthermore, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ₄₂.

Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils - a comparative study using MD simulations of 17-42 residues

Extracellular plaques, the hallmark of Alzheimer's disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 in silico mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization.Communicated by Ramaswamy H. Sarma.

Novel Amino Acid Assembly in the Silk Tubes of Arid-Adapted Segestriid Spiders

We investigated in different sites inside or outside the Namib Desert the amino acids composition of the protein material forming the tube silk of Ariadna spiders. These spiders belong to the primitive Segestriidae family and spend their life inside vertical silk burrows dug within the sandy and gravelly soil of arid areas. The silks, previously purified by solubilization in hexafluoroisopropanol, were subjected to partial or total acid hydrolysis. Partial hydrolyzed samples, analyzed by mass spectrometry (matrix assisted laser desorption/ionization and electrospray), led to relevant information on the amino acid sequences in the proteins. The free amino acids formed by complete hydrolysis were derivatized with the Marfey's reagent and characterized by electrospray mass spectrometry. The reconstruction of the amino acids highlights a homogeneous plan in the chemical structure of all the analyzed silks. Eight amino acids constituting the primary structure of the proteins were identified. Alanine and glycine are the most abundant ones, with a prevalence of alanine, constituting together at least 61% of the chemical composition of the protein material, differently from what occurs in known spidroins. High percentages of proline, serine and threonine and low percentages of leucine complete the peculiarity of these proteins. The purified silks were also characterized by Fourier-transform Infrared Spectroscopy and their thermal properties were investigated by differential scanning calorimetry. The comparison of the silk tubes among the various Namibian populations, carried out through a multivariate statistical analysis, shows significant differences in their amino acid assembly possibly due to habitat features.

Deleterious Variants in WNT10A, EDAR, and EDA Causing Isolated and Syndromic Tooth Agenesis: A Structural Perspective from Molecular Dynamics Simulations

The dental abnormalities are the typical features of many ectodermal dysplasias along with congenital malformations of nails, skin, hair, and sweat glands. However, several reports of non-syndromic/isolated tooth agenesis have also been found in the literature. The characteristic features of hypohidrotic ectodermal dysplasia (HED) comprise of hypodontia/oligodontia, along with hypohidrosis/anhidrosis, and hypotrichosis. Pathogenic variants in EDA, EDAR, EDARADD, and TRAF6, cause the phenotypic expression of HED. Genetic alterations in EDA and WNT10A cause particularly non-syndromic/isolated oligodontia. In the current project, we recruited 57 patients of 17 genetic pedigrees (A-Q) from different geographic regions of the world, including Pakistan, Egypt, Saudi Arabia, and Syria. The molecular investigation of different syndromic and non-syndromic dental conditions, including hypodontia, oligodontia, generalized odontodysplasia, and dental crowding was carried out by using exome and Sanger sequencing. We have identified a novel missense variant (c.311G>A; p.Arg104His) in WNT10A in three oligodontia patients of family A, two novel sequence variants (c.207delinsTT, p.Gly70Trpfs*25 and c.1300T>G; p.Try434Gly) in EDAR in three patients of family B and four patients of family C, respectively. To better understand the structural and functional consequences of missense variants in WNT10A and EDAR on the stability of the proteins, we have performed extensive molecular dynamic (MD) simulations. We have also identified three previously reported pathogenic variants (c.1076T>C; p.Met359Thr), (c.1133C>T; p.Thr378Met) and (c.594_595insC; Gly201Argfs*39) in EDA in family D (four patients), E (two patients) and F (one patient), correspondingly. Presently, our data explain the genetic cause of 18 syndromic and non-syndromic tooth agenesis patients in six autosomal recessive and X-linked pedigrees (A-F), which expand the mutational spectrum of these unique clinical manifestations.

Dynamic ion pair behavior stabilizes single α-helices in proteins

Ion pairs are key stabilizing interactions between oppositely charged amino acid side chains in proteins. They are often depicted as single conformer salt bridges (hydrogen-bonded ion pairs) in crystal structures, but it is unclear how dynamic they are in solution. Ion pairs are thought to be particularly important in stabilizing single α-helix (SAH) domains in solution. These highly stable domains are rich in charged residues (such as Arg, Lys, and Glu) with potential ion pairs across adjacent turns of the helix. They provide a good model system to investigate how ion pairs can contribute to protein stability. Using NMR spectroscopy, small-angle X-ray light scattering (SAXS), and molecular dynamics simulations, we provide here experimental evidence that ion pairs exist in a SAH in murine myosin 7a (residues 858-935), but that they are not fixed or long lasting. In silico modeling revealed that the ion pairs within this α-helix exhibit dynamic behavior, rapidly forming and breaking and alternating between different partner residues. The low-energy helical state was compatible with a great variety of ion pair combinations. Flexible ion pair formation utilizing a subset of those available at any one time avoided the entropic penalty of fixing side chain conformations, which likely contributed to helix stability overall. These results indicate the dynamic nature of ion pairs in SAHs. More broadly, thermodynamic stability in other proteins is likely to benefit from the dynamic behavior of multi-option solvent-exposed ion pairs.

Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study

One of the fundamental events in protein folding is α-helix formation, which involves sequential development of a series of helical hydrogen bonds between the backbone C═O group of residues i and the -NH group of residues i + 4. While we now know a great deal about α-helix folding dynamics, a key question that remains to be answered is where the productive helical nucleation event occurs. Statistically, a helical nucleus (or the first helical hydrogen-bond) can form anywhere within the peptide sequence in question; however, the one that leads to productive folding may only form at a preferred location. This consideration is based on the fact that the α-helical structure is inherently asymmetric, due to the specific alignment of the helical hydrogen bonds. While this hypothesis is plausible, validating it is challenging because there is not an experimental observable that can be used to directly pinpoint the location of the productive nucleation process. Therefore, in this study we combine several techniques, including peptide cross-linking, laser-induced temperature-jump infrared spectroscopy, and molecular dynamics simulations, to tackle this challenge. Taken together, our experimental and simulation results support an α-helix folding mechanism wherein the productive nucleus is formed at the N-terminus, which propagates toward the C-terminal end of the peptide to yield the folded structure. In addition, our results show that incorporation of a cross-linker can lead to formation of differently folded conformations, underscoring the need for all-atom simulations to quantitatively assess the proposed cross-linking design.

Dissecting the mechanism of action of actinoporins. Role of the N-terminal amphipathic α-helix in membrane binding and pore activity of sticholysins I and II

Actinoporins sticholysin I and sticholysin II (St I, St II) are proposed to lyse model and biomembranes via toroidal pore formation by their N-terminal domain. Based on the hypothesis that peptide fragments can reproduce the structure and function of this domain, the behavior of peptides containing St I residues 12–31 (StI_12-31), St II residues 11–30 (StII_11-30), and its TOAC-labeled analogue (N-TOAC-StII_11-30) was examined. Molecular modeling showed a good match with experimental structures, indicating amphipathic α-helices in the same regions as in the toxins. CD spectra revealed that the peptides were essentially unstructured in aqueous solution, acquiring α-helical conformation upon interaction with micelles and large unilamellar vesicles (LUV) of variable lipid composition. Fluorescence quenching studies with NBD-containing lipids indicated that N-TOAC-StII_11-30’s nitroxide moiety is located in the membranes polar head group region. Pyrene-labeled phospholipid inter-leaflet redistribution suggested that the peptides form toroidal pores, according to the mechanism of action proposed for the toxins. Binding occurred only to negatively charged LUV, indicating the importance of electrostatic interactions; in contrast the peptides bound to both negatively charged and zwitterionic micelles, pointing to a lesser influence of these interactions. In addition, differences between bilayers and micelles in head group packing and in curvature led to differences in peptide-membrane interaction. We propose that the peptides topography in micelles resembles that of the toxins in the toroidal pore. The peptides mimicked the toxins permeabilizing activity, St II peptides being more effective than StI_12-31. To our knowledge, this is the first demonstration that differences in the toxins N-terminal amphipathic α-helix play a role in the difference between St I and St II activities.

Nitrite ion modifies tyrosine and lysine residues of extracellular matrix proteins

Age-related macular degeneration (AMD) is a disease characterized by degenerative changes in the retinal pigment epithelium and Bruch's membrane. Inflammation is considered a major risk factor for the development and progression of AMD. Nitrite is a potent byproduct of inflammation and has been detected at elevated concentrations in AMD donor tissue. We hypothesize that nitrite chemically modifies the extracellular matrix (ECM) of Bruch's membrane as an initial step to degenerative changes observed in AMD. Non-enzymatically nitrated synthetic ECM peptides, fibronectin and laminin, were used as model systems for inflammation. Using LC/MS, we identified that nitration preferentially occurred on tyrosine and deamination of lysine under the studied conditions. At tyrosine residues, 3-nitrotyrosine was produced and shifted the total mass by the addition of 45 amu. Deamination of lysine occurred and resulted in the formation of either an alkene or alcohol group. The alkene group was observed with a loss of 17 amu. An addition of 1 amu was observed with alcohol formation. We hypothesize that these initial chemical modifications to the structure of ECM proteins may be the responsible for altering the structure and consequent function of Bruch's membrane.

Shielding effect in protein folding

One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly.

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics

Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.

N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH₂ ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH₂ ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH₂ ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.

Microscopic nucleation and propagation rates of an alanine-based α-helix

An infrared temperature-jump (T-jump) study by Huang et al. (Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 2788-2793) showed that the conformational relaxation kinetics of an alanine-based α-helical peptide depend not only on the final temperature (Tf) but also on the initial temperature (Ti) when Tf is fixed. Their finding indicates that the folding free energy landscape of this peptide is non-two-state like, allowing for the population of conformational ensembles with different helical lengths and relaxation times in the temperature range of the experiment. Because α-helix folding involves two fundamental events, nucleation and propagation, the results of Huang et al. thus present a unique opportunity to determine their rate constants - a long-sought goal in the study of the helix-coil transition dynamics. Herein, we capitalize on this notion and develop a coarse-grained kinetic model to globally fit the thermal unfolding curve and T-jump kinetic traces of this peptide. Using this strategy, we are able to explicitly determine the microscopic rate constants of the kinetic steps encountered in the nucleation and propagation processes. Our results reveal that the time taken to form one α-helical turn (i.e., an α-helical segment with one helical hydrogen bond) is about 315 ns, whereas the time taken to elongate this nucleus by one residue (or backbone unit) is 5.9 ns, depending on the position of the residue.

In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome

Natowicz syndrome (mucopolysaccharidoses type 9) is a lysosomal storage disorder caused by deficient or defective human hyaluronidase 1. The disorder is not well studied at the molecular level. Therefore, a new in silico approach was proposed to study the molecular basis on which one clinically observed mutation, Glu268Lys, results in a defective enzyme. The native and mutant structures were subjected to comparative analyses using a conformational sampling approach for geometrical variables viz, RMSF, RMSD, and Ramachandran plot. In addition, the strength of a Cys207-Cys221 disulfide bond and electrostatic interaction between Arg265 and Asp206 were studied, as they are known to be involved in the catalytic activity of the enzyme. Native and mutant E268K showed statistically significant variations with p < 0.05 in RMSD, Ramachandran plot, strengths of disulfide bond, and electrostatic interactions. Further, single model analysis showed variations between native and mutant structures in terms of intra-protein interactions, hydrogen bond dilution, secondary structure, and dihedral angles. Docking analysis predicted the mutant to have a less favorable substrate binding energy compared to the native protein. Additionally, steered MD analysis indicated that the substrate should have more affinity to the native than mutant enzymes. The observed changes theoretically explain the less favorable binding energy of substrate towards mutant E268K, thereby providing a structural basis for its reduced catalytic activity. Hence, our study provides a basis for understanding the disruption in the molecular mechanism of human hyaluronidase 1 by mutation E268K, which may prove useful for the development of synthetic chaperones as a treatment option for Natowicz syndrome.

Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics

Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization.

Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water

Dynamic combinatorial chemistry was used to generate a set of receptors for peptides containing methylated lysine (KMen, n = 0-3) and study the contribution of electrostatic effects and pocket depth to binding affinity and selectivity. We found that changing the location of a carboxylate resulted in an increase in preference for KMe2, presumably based on ability to form a salt bridge with KMe2. The number of charged groups on either the receptor or peptide guest systematically varied the binding affinities to all guests by approximately 1-1.5 kcal mol(-1), with little influence on selectivity. Lastly, formation of a deeper pocket led to both increased affinity and selectivity for KMe3 over the lower methylation states. From these studies, we identified that the tightest binder was a receptor with greater net charge, with a Kd of 0.2 μM, and the receptor with the highest selectivity was the one with the deepest pocket, providing 14-fold selectivity between KMe3 and KMe2 and a Kd for KMe3 of 0.3 μM. This work provides key insights into approaches to improve binding affinity and selectivity in water, while also demonstrating the versatility of dynamic combinatorial chemistry for rapidly exploring the impact of subtle changes in receptor functionality on molecular recognition in water.

Structural conservation of the short α-helix in modified higher and lower polarity water solutions

Which conformation is preferred when the polarity of water molecules is scaled byE_P=E_LJ+S²E_C?

Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study

The structure of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in explicit aqueous solutions with mixed inorganic salts (NaCl and KCl) is investigated by using molecular simulations. The concentration of Na(+), c(Na(+)), varies from 0.0M to 1.0M, whereas the concentration of K(+) is 1-c(Na(+)). The simulated peptide is very sensitive to the change of concentration ratio between Na(+) and K(+). When the concentration ratio between Na^{+} and K^{+} is changed from 0.5/0.5, the structure of the peptide becomes loose or disordered. This specific phenomenon is confirmed via checking the changes of helix parameters and mapping the free energy along different coordinates. The higher normalized probability of forming direct and indirect salt bridges between residues Glu7(+) and Lys11(+) and the smallest probability of forming ringlike structures should be responsible for the stabilized helix structure in the 0.5 Na(+)/0.5 K(+) solution. Furthermore, a noticeable conformational transition from an extended helix to an α helix is found in the 0.5 Na(+)/0.5 K(+) solution, where a local ion cloud shows that some Na(+) ions in the inner shells are still directly binding with the peptide, while K(+) in the outer shells are moving into the inner shells, keeping the peptide in the collapsed state.

Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations

We have investigated effects of salt ions on folding events of a helical miniprotein chicken villin headpiece subdomain HP36. Low concentrations of ions alter electrostatic interactions between charged groups of a protein and can change the populations of conformers. Here, we compare two data sets of folding simulations of HP36 in explicit water solvent with or without ions. For efficient sampling of the conformational space of HP36, the multicanonical replica-exchange molecular dynamics method was employed. Our analyses suggest that salt alters salt-bridging nature of the protein at later stages of folding at room temperature. Especially, more nonnative, nonlocal salt bridges are formed at near-native conformations in pure water. Our analyses also show that such salt-bridge formation hinders the fully native hydrophobic-core packing at the final stages of folding.

Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α→β transition in full protein context

An α→β transition underlies the first step of disease causing amyloidogenesis in many proteins. In view of this, many studies have been carried out using peptide models to characterize these secondary structural transitions. In this paper we show that an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme (M. Sagermann, W. A. Baase and B. W. Matthews, Proc. Natl. Acad. Sci. U.S.A., 1999, 96, 6078) displays an α→β transition. We performed molecular dynamics (MD) simulation of L20, using the GROMACS package of programs and united atom GROMOS 53a6 force field for a time period of 600 ns at 300 K, in explicit water. Our MD simulation demonstrated that the transition occurs in a duplicated α-helical region inserted tandemly at the N-terminus of the 'parent' helix. We show that a C-terminal β-sheet anchors the parent helix while the loosely held N-terminal loop in the duplicate region is vulnerable to solvent attack and thus undergoes an α→β transition. Main chain-solvent interactions were seen to stabilize the observed β-structure. Thus L20 serves as a good protein model for characterization of α→β transition in a full length protein.

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the α-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures-corrections that capture many-body effects missing from an energy surface fitted to gas phase calculations on dipeptides. The experimental temperature dependence of helix formation in (AAQAA)(3) and parameters for helix nucleation and elongation are in much better agreement with experiment than those obtained with other recent force fields. In contrast, CMAP parameters derived by fitting to a vacuum quantum mechanical surface for the alanine dipeptide do not reproduce the enhanced cooperativity, showing that the empirical backbone corrections, and not some other feature of the force field, are responsible. We also find that the cooperativity of β-hairpin formation is much improved relative to other force fields we have studied. Comparison with (ϕ,ψ) distributions from the Protein Data Bank further justifies the inclusion of many-body effects in the CMAP. These results suggest that the revised energy function will be suitable for both simulations of unfolded or intrinsically disordered proteins and for investigating protein-folding mechanisms.

Temperature dependence of water interactions with the amide carbonyls of α-helices

Hydration is a key determinant of the folding, dynamics, and function of proteins. In this study, temperature-dependent Fourier transform infrared (FTIR) spectroscopy combined with singular value decomposition (SVD) and global fitting were used to investigate both the interaction of water with α-helical proteins and the cooperative thermal unfolding of these proteins. This methodology has been applied to an isolated α-helix (Fs peptide) and to globular α-helical proteins including the helical subdomain and full-length villin headpiece (HP36 and HP67). The results suggest a unique IR signature for the interaction of water with the helical amide carbonyl groups of the peptide backbone. The IR spectra indicate a weakening of the net hydrogen bond strength of water to the backbone carbonyls with increasing temperature. This weakening of the backbone solvation occurs as a discrete transition near the maximum of the temperature-dependent hydrophobic effect, not a continuous change with increasing temperature. Possible molecular origins of this effect are discussed with respect to previous molecular dynamics simulations of the temperature-dependent solvation of the helix backbone.

50 Years of Lifson-Roig Models: Application to Molecular Simulation Data

Simple helix-coil transition theories have been indispensable tools in the analysis of data reporting on the reversible folding of α-helical polypeptides. They provide a transferable means to not only characterize different systems but to also compare different techniques, viz., experimental probes monitoring helix-coil transitions in vitro or biomolecular force fields in silico. This article addresses several issues with the application of Lifson-Roig theory to helix-coil transition data. We use computer simulation to generate two sets of ensembles for the temperature-controlled, reversible folding of the 21-residue, alanine-rich FS peptide. Ensembles differ in the rigidity of backbone bond angles and are analyzed using two distinct descriptors of helicity. The analysis unmasks an underlying phase diagram that is surprisingly complex. The complexities give rise to fitted nucleation and propagation parameters that are difficult to interpret and that are inconsistent with the distribution of isolated residues in the α-helical basin. We show that enthalpies of helix formation are more robustly determined using van't Hoff analysis of simple measures of helicity rather than fitted propagation parameters. To overcome some of these issues, we design a simple variant of the Lifson-Roig model that recovers physical interpretability of the obtained parameters by allowing bundle formation to be described in simple fashion. The relevance of our results is discussed in relation to the applicability of Lifson-Roig models to both in silico and in vitro data.

Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece

The increasing accuracy of molecular dynamics force fields parameters and the increasing resolution of experimental results allow one to carefully compare and complement in silico data with experimental observations. Here, we study the human villin headpiece C-terminal helical subdomain (HP35) with the recent highly optimized Amber99SB*-ILDN force field and compare the results with recent high resolution triplet-triplet energy transfer (TTET) experiments. The correct reproduction of the main structural features reveals a good agreement between experimental data and simulations.

The role of hydrophobic surfaces in altering water-mediated peptide-peptide interactions in an aqueous environment

Using Born-Oppenheimer molecular dynamics within the density functional framework, we calculated the effective force acting on water-mediated peptide-peptide interaction between antiparallel β-sheets in an aqueous environment and also in the vicinity of a hydrophobic surface. From the magnitude of the effective force (corresponding to the slope of the free energy as a function of the interpeptide distance) and its sign (a negative value indicates an effective attraction, whereas a positive value indicates an effective repulsion) we can elucidate the fundamental differences of the water-mediated peptide-peptide interactions in those two environments. The computed effective forces indicate that the water-mediated interaction between peptides in an aqueous environment is attractive in the range of interpeptide distance d = 7-8 Å when hydrophobic surfaces are not nearby. Due to the stabilization of the water molecules bridging between the two β-sheets, a free energy barrier exists between the direct and indirect (water-mediated) interpeptide interactions. However, when the peptides are in the proximity of hydrophobic surfaces, this free energy barrier decreases because the hydrophobic surfaces enhance the interpeptide attraction by the destabilization and ease-to-libration of the bridging water molecules between them.

Direct assessment of the α-helix nucleation time

The nucleation event in α-helix formation is a fundamental process in protein folding. However, determining how quickly it takes place based on measurements of the relaxation dynamics of helical peptides is difficult because such relaxations invariably contain contributions from various structural transitions such as from helical to nonhelical states and helical to partial-helical conformations. Herein, we measure the temperature-jump (T-jump) relaxation kinetics of three model peptides that fold into a single-turn α-helix, using time-resolved infrared spectroscopy, aiming to provide a direct assessment of the helix nucleation rate. The α-helical structure of these peptides is stabilized by a covalent cross-linker formed between the side chains of two residues at the i and i + 4 positions. If we assume that this cross-linker mimics the structural constraint arising from a strong side chain-side chain interaction (e.g., a salt bridge) in proteins, these peptides would represent good models for studying the nucleation process of an α-helix in a protein environment. Indeed, we find that the T-jump induced relaxation rate of these peptides is approximately (0.6 μs)(-1) at room temperature, which is slower than that of commonly studied alanine-based helical peptides but faster than that of a naturally occurring α-helix whose folded state is stabilized by a series of side chain-side chain interactions. Taken together, our results put an upper limit of about 1 μs for the helix nucleation time at 20 °C and suggest that the subsequent propagation steps occur with a time constant of about 240 ns.

Circular dichroism and ultraviolet resonance Raman indicate little Arg-Glu side chain α-helix peptide stabilization

Electrostatic interactions between side chains can control the conformation and folding of peptides and proteins. We used circular dichroism (CD) and ultraviolet (UV) resonance Raman spectroscopy (UVRR) to examine the impact of side chain charge on the conformations of two 21 residue mainly polyala peptides with a few Arg and Glu residues. We expected that attractions between Arg-10 and Glu-14 side chains would stabilize the α-helix conformation compared to a peptide with an Arg-14. Surprisingly, CD suggests that the peptide with the Glu-14 is less helical. In contrast, the UVRR show that these two peptides have similar α-helix content. We conclude that the peptide with Glu-14 has the same net α-helix content as the peptide with the Arg but has two α-helices of shorter length. Thus, side chain interactions between Arg-10 and Glu-14 have a minor impact on α-helix stability. The thermal melting of these two peptides is similar. However the Glu-14 peptide pH induced melting forms type III turn structures that form α-helix-turn-α-helix conformations.

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

Conventional molecular dynamics simulations on 50 ns to 1 μs time scales were used to study the effects of explicit solvent models on the conformational behavior and solvation of two oligopeptide solutes: α-helical EK-peptide (14 amino acids) and a β-hairpin chignolin (10 amino acids). The widely used AMBER force fields (ff99, ff99SB, and ff03) were combined with four of the most commonly used explicit solvent models (TIP3P, TIP4P, TIP5P, and SPC/E). Significant differences in the specific solvation of chignolin among the studied water models were identified. Chignolin was highly solvated in TIP5P, whereas reduced specific solvation was found in the TIP4P, SPC/E, and TIP3P models for kinetic, thermodynamic, and both kinetic and thermodynamic reasons, respectively. The differences in specific solvation did not influence the dynamics of structured parts of the folded peptide. However, substantial differences between TIP5P and the other models were observed in the dynamics of unfolded chignolin, stability of salt bridges, and specific solvation of the backbone carbonyls of EK-peptide. Thus, we conclude that the choice of water model may affect the dynamics of flexible parts of proteins that are solvent-exposed. On the other hand, all water models should perform similarly for well-structured folded protein regions. The merits of the TIP3P model include its high and overestimated mobility, which accelerates simulation processes and thus effectively increases sampling.

How the diffusivity profile reduces the arbitrariness of protein folding free energies

The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an alpha-helix in explicit water solvent as it stochastically folds and unfolds. The free-energy profiles for different RCs exhibit significant variations, some having an activation barrier, while others not. We show that this variation has little effect on the predicted folding kinetics if the diffusivity profiles are properly taken into account. This kinetic quasi-universality is rationalized by an RC rescaling, which, due to the reparameterization invariance of the Fokker-Planck equation, allows the combination of free-energy and diffusivity effects into a single function, the rescaled free-energy profile. This rescaled free energy indeed shows less variation among different RCs than the bare free energy and diffusivity profiles separately do, if we properly distinguish between RCs that contain knowledge of the native state and those that are purely geometric in nature. Our method for extracting diffusivity profiles is easily applied to experimental single molecule time series data and might help to reconcile conflicts that arise when comparing results from different experimental probes for the same protein.

Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors

Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large-scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, scientists have returned to exploring the power of graphics processing units (GPUs) for various applications, such as MD, enabled by the recent advances in hardware and integrated programming interfaces such as NVIDIA's CUDA platform. One area of particular interest within the context of chemical applications is that of aqueous interfaces, the salt solutions of which have found application as model systems for studying atmospheric process as well as physical behaviors such as the Hoffmeister effect. Here, we present results of GPU-accelerated simulations of the liquid-vapor interface of aqueous sodium iodide solutions. Analysis of various properties, such as density and surface tension, demonstrates that our model is consistent with previous studies of similar systems. In particular, we find that the current combination of water and ion force fields coupled with the ability to simulate surfaces of differing area enabled by GPU hardware is able to reproduce the experimental trend of increasing salt solution surface tension relative to pure water. In terms of performance, our GPU implementation performs equivalent to CHARMM running on 21 CPUs. Finally, we address possible issues with the accuracy of MD simulaions caused by nonstandard single-precision arithmetic implemented on current GPUs.

Amyloid-beta42 oligomer structures from fibrils: a systematic molecular dynamics study

Recent experimental data demonstrate that small, soluble amyloid-beta42 oligomers play an important role in Alzheimer's disease because they exhibit neurotoxic properties and also act as seed for fibril growth. We performed all-atom molecular dynamics simulations in explicit solvent of 0.7 micros in total on five Abeta9-42 oligomers (monomer through pentamer) starting from the fibril conformation. The initial conformation proves to be stable in the trimer to pentamer, and the two parallel in-register beta-sheets as well as the connecting turn are preserved. The dimer undergoes larger conformational changes in its C-terminus, and the predominant conformation detected exhibits an additional antiparallel beta-sheet in one of the subunits. This conformational rearrangement allows efficient shielding of hydrophobic residues from the solvent, which is not possible for a dimer in the fibril conformation. In addition to the presence of the hydrogen bonds in the beta-sheets, the larger oligomers are stabilized by interchain D23-K28 salt bridges, whereas a D23-N27 interaction is found in the dimer. The degree of structural similarity to the fibril conformation detected for the oligomers in the simulation may also offer a structural explanation for the experimental finding that trimers and tetramers act as more potent seeds in fibril formation than dimers because only small conformational changes will be required for fibril growth. The fact that the dimer predominantly exists in conformations distinct from the larger oligomers and the fibril is also interesting for the design of anti-Alzheimer drugs, because it suggests that multiple drugs might be required to target the structurally different neurotoxic oligomers.

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.