Relationship of sidechain hydrophobicity and α-helical propensity on the stability of the single-stranded amphipathic α-helix

The aim of the present investigation is to determine the effect of α-helical propensity and sidechain hydrophobicity on the stability of amphipathic α-helices. Accordingly, a series of 18-residue amphipathic α-helical peptides has been synthesized as a model system where all 20 amino acid residues were substituted on the hydrophobic face of the amphipathic α-helix. In these experiments, all three parameters (sidechain hydrophobicity, α-helical propensity and helix stability) were measured on the same set of peptide analogues. For these peptide analogues that differ by only one amino acid residue, there was a 0.96 kcal/mole difference in α-helical propensity between the most (Ala) and the least (Gly) α-helical analogue, a 12.1-minute difference between the most (Phe) and the least (Asp) retentive analogue on the reversed-phase column, and a 32.3°C difference in melting temperatures between the most (Leu) and the least (Asp) stable analogue. The results show that the hydrophobicity and α-helical propensity of an amino acid sidechain are not correlated with each other, but each contributes to the stability of the amphipathic α-helix. More importantly, the combined effects of α-helical propensity and sidechain hydrophobicity at a ratio of about 2:1 had optimal correlation with α-helix stability. These results suggest that both α-helical propensity and sidechain hydrophobicity should be taken into consideration in the design of α-helical proteins with the desired stability.     

Secondary structure induction in aqueous vs membrane-like environments

The conformational propensity of the 20 naturally occurring amino acids was determined in aqueous 3-[N-morpholino]propane-sulfonic acid (MOPS) buffer, protein interior-like [nonmicellar sodium dodecylsulfate (SDS)] and membrane-like environments (micellar SDS and lysophosphatidylglycerol/lysophosphatidylcholine micelles) using a single “guest” position in a polyalanine-based model host peptide (Ac-KYA₁₃K-NH₂). This model system allows the intrinsic α-helical or β-sheet propensity of the amino acids to be determined without intra- and interchain side chain interactions. The overall environment dependence observed for the conformational propensity for the amino acids studied confirms the importance of determining propensity in lipidic environments to better elucidate the biological functions of proteins. The hydrophobic interactions between peptide side chains and lipids appeared to be the primary forces driving the conformational induction in lipidic environments of the model peptides studied. Finally, when comparing the results of these studies with those reported in the literature, the local environment was found to highly influence 65% of the 20 naturally occurring amino acids. © 1997 John Wiley & Sons, Inc. Biopoly 42: 489–498, 1997     

Amphiphilic ��-Helical Potential: A Putative Folding Motif Adding Few Constraints to Protein Evolution

Evidence from a number of studies indicates that protein folding is dictated not only by factors stabilizing the native state, but also by potentially independent factors that create folding pathways. How natural selection might cope simultaneously with two independent factors was addressed in this study within the framework of the "Lim-model" of protein folding, which postulates that the early stages of folding of all globular proteins, regardless of their native structure, are directed at least in part by potential to form amphiphilic α-helices. For this purpose, the amphiphilic α-helical potential in randomly ordered amino acid sequences and the conservation in phylogeny of amphiphilic α-helical potential within various proteins were assessed. These analyses revealed that amphiphilic α-helical potential is a common occurrence in random sequences, and that the presence of amphiphilic α-helical potential is present but not conserved in phylogeny within a given protein. The results suggest that the rapid formation of molten globules and the variable behavior of those globules depending on the protein may be a fundamental property of polymers of naturally occurring amino acids more so than a trait that must be derived or maintained by natural selection. Further, the results point toward the utility of randomly occurring process in protein function and evolution, and suggest that the formation of efficient pathways that determine early processes in protein folding, unlike the formation of stable, native protein structure, does not present a substantial hurdle during the evolution of amino acid sequences.     

Correlations in Protein Sequences and Property Codes

Correlation functions in large sets of non-homologous protein sequences are analysed. Finite size corrections are applied and fluctuations are estimated. As symbol sequences have to be mapped to sequences of numbers to calculate correlation functions, several property codes are tested as such mappings. We found hydrophobicity autocorrelation functions to be strongly oscillating. Another strong signal is the monotonously decaying α-helix propensity autocorrelation function. Furthermore, we detected signals corresponding to an alteration of positively and negatively charged residues at a distance of 3–4 amino acids.To look beyond the property codes gained by the methods of physical chemistry, mappings yielding a strong correlation signal are sought for using a Monte Carlo simulation. The mappings leading to strong signals are found to be related to hydrophobicity of α-helix propensity. A cluster analysis of the top scoring mappings leads to two novel property codes. These two property codes are gained from sequence data only. They turn out to be similar to known property codes for hydrophobicity or polarity.     

Changes of net charge and α-helical content affect the pharmacokinetic properties of human serum albumin

The pharmacokinetics of 17 genetic variants of human serum albumin with single-residue mutations and their corresponding normal albumin were studied in mice. In all cases, the plasma half-life was affected, but only variants with + 2 changes in charge prolonged it, whereas changes in hydrophobicity decreased it. Good positive and negative correlations were found between changes in α-helical content taking place in domains I + III and domain II, respectively, and changes in half-lives. No correlation was found to type of mutation or to changes in heat stability as represented by ΔH_v. Liver and kidney uptake clearances were also modified: α-helical changes of domains I + III showed good negative correlations to both types of clearances, whereas changes in domain II only had a good positive correlation to kidney uptake clearance. No correlation between the other molecular changes and organ uptakes was observed. The relatively few correlations between changes in molecular characteristics and the organ uptakes of the variants are most probably due to different handling by plasma enzyme(s) and the various types of cell endocytosis. Of the latter, most lead to destruction of albumin, but at least one results in recycling of the protein. The present information should be useful when designing recombinant, therapeutical albumins or albumin products with a modified plasma half-life.     

An obligatory alpha-helical amino acid residue

Stereochemical studies predict that α-amino isobutyric acid, one of the amino acids found in antibiotics, can fold only into left- or righthanded α-helical conformations. Such residues will direct chain folding and should be useful in synthetic analogs of protein sequences to increase helix stability.     

Role of sequence and structure of the hendra fusion protein fusion Peptide in membrane fusion

Viral fusion proteins are intriguing molecular machines that undergo drastic conformational changes to facilitate virus-cell membrane fusion. During fusion a hydrophobic region of the protein, termed the fusion peptide (FP), is inserted into the target host cell membrane, with subsequent conformational changes culminating in membrane merger. Class I fusion proteins contain FPs between 20 and 30 amino acids in length that are highly conserved within viral families but not between. To examine the sequence dependence of the Hendra virus (HeV) fusion (F) protein FP, the first eight amino acids were mutated first as double, then single, alanine mutants. Mutation of highly conserved glycine residues resulted in inefficient F protein expression and processing, whereas substitution of valine residues resulted in hypofusogenic F proteins despite wild-type surface expression levels. Synthetic peptides corresponding to a portion of the HeV F FP were shown to adopt an α-helical secondary structure in dodecylphosphocholine micelles and small unilamellar vesicles using circular dichroism spectroscopy. Interestingly, peptides containing point mutations that promote lower levels of cell-cell fusion within the context of the whole F protein were less α-helical and induced less membrane disorder in model membranes. These data represent the first extensive structure-function relationship of any paramyxovirus FP and demonstrate that the HeV F FP and potentially other paramyxovirus FPs likely require an α-helical structure for efficient membrane disordering and fusion.     

Hydrophobicity Density Profiles to Predict Thermal Stability Enhancement in Proteins

A hydrophobicity density is defined for a protein through its hydrophobicity tensor (similar to the inertia tensor), by using the Eisenberg hydrophobicity scale of the hydrophobic amino acids of a protein. This allows calculation of the radii of the corresponding hydrophobic ellipsoid of a protein and thus subsequently of its hydrophobic density. A hydrophobicity density profile is then obtained by simulating point mutations of each amino acid of a protein either to a high hydrophobicity value or to zero hydrophobicity. It is found that an increase in the hydrophobic density of the protein correlates with an increase of its mid-point transition temperature. From this profile it is possible to determine the amino acids or domain stretches in a protein that are most amenable to mutation in order to increase the thermal stability. The model is tested to predict the thermostabilisation effects of two mutations in a β-glucanase: M29G and M29F. This model is compared with other hydrophobicity-related profiles described by other authors.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Codon Bias and Mutability in HIV Sequences

A survey of the patterns of synonymous codon preference in the HIV env gene reveals a correlation between the codon bias and the mutability requirements of different regions of the protein. At hypervariable regions in gp120 one finds a greater proportion of codons that tend to mutate nonsynonymously, but to a target that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective pressure placed on the virus by the induced immune response, which favors amino acid substitutions in the complementarity determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein. Received: 9 June 1997 / Accepted: 25 May 1998     

Phosphoprotein and nucleocapsid protein evolution of vesicular stomatitis virus New Jersey.

The entire phosphoprotein (P) and nucleocapsid (N) protein gene sequences and deduced amino acid sequences for 18 selected vesicular stomatitis virus isolates representative of the natural genetic diversity within the New Jersey serotype are reported. Phylogenetic analysis of the data using maximum parsimony allowed construction of evolutionary trees for the individual genes and the combined N, P, and glycoprotein (G) genes of these viruses. Virtually identical rates of nucleotide substitutions were found for each gene, indicating that evolution of these genes occurs at essentially the same rate. Although up to 19 and 17% sequence differences were evident in the P and N genes, respectively, no variation in gene length or evidence of recombinational rearrangements was found. However, striking evolutionary differences were observed among the amino acid sequences of vesicular stomatitis virus New Jersey N, P, and G proteins. The N protein amino acid sequence was the most highly conserved among the different isolates, indicating strong functional and structural constraints. Conversely, the P protein amino acid sequences were highly variable, indicating considerably fewer constraints or greater evolutionary pressure on the P protein. Much of the remarkable amino acid variability of the P protein resided in a hypervariable domain located between amino acids 153 and 205. The variability within this region would be consistent with it playing a structural role as a spacer to maintain correct conformational presentation of the separate active domains of this multifunctional protein. In marked contrast, the adjacent domain I of the P protein (previously thought to be under little evolutionary constraint) contained a highly conserved region. The colocalization of a short, potentially functional overlapping open reading frame to this region may explain this apparent anomaly.     

The First N-terminal Amino Acids of α-Synuclein Are Essential for α-Helical Structure Formation In Vitro and Membrane Binding in Yeast

α-Synuclein (α-syn), a protein implicated in Parkinson's disease, is structurally diverse. In addition to its random-coil state, α-syn can adopt an α-helical structure upon lipid membrane binding or a β-sheet structure upon aggregation. We used yeast biology and in vitro biochemistry to detect how sequence changes alter the structural propensity of α-syn. The N-terminus of the protein, which adopts an α-helical conformation upon lipid binding, is essential for membrane binding in yeast, and variants that are more prone to forming an α-helical structure in vitro are generally more toxic to yeast. β-Sheet structure and inclusion formation, on the other hand, appear to be protective, possibly by sequestering the protein from the membrane. Surprisingly, sequential deletion of residues 2 through 11 caused a dramatic drop in α-helical propensity, vesicle binding in vitro, and membrane binding and toxicity in yeast, part of which could be mimicked by mutating aspartic acid at position 2 to alanine. Variants with distinct structural preferences, identified here by a reductionist approach, provide valuable tools for elucidating the nature of toxic forms of α-syn in neurons.     

Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins

The pattern of amino acid substitutions and sequence conservation over many structure-based alignments of protein sequences was analyzed as a function of percentage sequence identity. The statistics of the amino acid substitutions were converted into the form of log-odds amino acid substitution matrices to which eigenvalue decomposition was applied. It was found that the most important component of the substitution matrices exhibited a sharp transition at the sequence identity of 30-35%, which coincides with the twilight zone. Above the transition point, the most dominant component is related to the mutability of amino acids and it acts to disfavor any substitutions, whereas below the transition point, the most dominant component is related to the hydrophobicity of amino acids and substitutions between residues of similar hydrophobic character are positively favored. Implications for protein evolution and sequence analysis are discussed.     

The signal distinguishing between targeting of outer membrane β-barrel protein to plastids and mitochondria in plants

The proteome of the outer membrane of mitochondria and chloroplasts consists of membrane proteins anchored by α-helical or β-sheet elements. While proteins with α-helical transmembrane domains are present in all cellular membranes, proteins with β-barrel structure are specific for these two membranes. The organellar β-barrel proteins are encoded in the nuclear genome and thus, have to be targeted to the outer organellar membrane where they are recognized by surface exposed translocation complexes. In the last years, the signals that ensure proper targeting of these proteins have been investigated as essential base for an understanding of the regulation of cellular protein distribution. However, the organellar β-barrel proteins are unique as most of them do not contain a typical targeting information in form of an N-terminal cleavable targeting signal. Recently, it was discovered that targeting and surface recognition of mitochondrial β-barrel proteins in yeast, humans and plants depends on the hydrophobicity of the last β-hairpin of the β-barrel. However, we demonstrate that the hydrophobicity is not sufficient for the discrimination of targeting to chloroplasts or mitochondria. By domain swapping between mitochondrial and chloroplast targeted β-barrel proteins atVDAC1 and psOEP24 we demonstrate that the presence of a hydrophilic amino acid at the C-terminus of the penultimate β-strand is required for mitochondrial targeting. A mutation of the chloroplast β-barrel protein psOEP24 which mimics such profile is efficiently targeted to mitochondria. Thus, we present the properties of the signal for mitochondrial targeting of β-barrel proteins in plants.     

β2-Strand of salivary S cystatins: A “chemeleon sequence”

Secondary structure prediction of salivary cystatins S, SA, and SN carried out by several methods label the 39-58 sequence (β2-strand) as predominantly α-helical. The helical propensity of a peptide corresponding to β2-strand of salivary SA cystatin analyzed by CD display high helical propensity in aqueous solution, whereas peptides matching the β2-strand amino acid sequence of cystatins S and SN, display random coil conformation in aqueous solution but acquire α-helical conformation in the presence of trifluoroethanol (TFE). Moreover molecular dynamics simulation performed on the homology modeling of cystatin SA constructed on the basis of recently determined three-dimensional structure of salivary cystatin D, suggests that cystatin SA does not significantly deviate from the starting structure over the course of the simulation. The results obtained indicate that the β2-strand of salivary S cystatins has high helical propensity when isolated from native protein and acquire the final β structure by interaction with the rest of the polypeptide chain.     

Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation

During protein evolution, amino acids change due to a combination of functional constraints and genetic drift. Proteins frequently contain pairs of amino acids that appear to change together (covariation). Analysis of covariation from naturally occurring sets of orthologs cannot distinguish between residue pairs retained by functional requirements of the protein and those pairs existing due to changes along a common evolutionary path. Here, we have separated the two types of covariation by independently recombining every naturally occurring amino acid variant within a set of 15 subtilisin orthologs. Our analysis shows that in this family of subtilisin orthologs, almost all possible pairwise combinations of amino acids can coexist. This suggests that amino acid covariation found in the subtilisin orthologs is almost entirely due to common ancestral origin of the changes rather than functional constraints. We conclude that naturally occurring sequence diversity can be used to identify positions that can vary independently without destroying protein function.     

Local-scale repetitiveness in amino acid use in eukaryote protein sequences: a genomic factor in protein evolution

We showed previously that the use of arginine versus lysine residues in eukaryote proteins is correlated positively with local GC content of the genome within approximately 50 residues. Cumulative analyses show that the tendency for self-clustering (or repetitive use) generally is the case for all types of amino acids except for certain hydrophobic types. The degree to which each of the amino acids is used recurrently is weak for ancient proteins (or protein domains), those that are conserved through both eukaryotes and prokaryotes, but strong for modern proteins, which are unique to organisms of particular phyla. These findings support the idea that repetitiveness occurs due to a propensity of genomic DNA to cause tandem genomic duplication. A protein sequence with high repetitiveness tends to be unique in the homology search, which may indicate the weaker constraints and, hence, more arbitrary use of amino acids. Simulation analyses suggest that tandem gene duplications on a very small scale (1 or 2 codons) is an important causal factor in maintaining repetitiveness in the presence of concomittant occurrence of substitutive point mutation. For yeast proteins, approximately 1.3 duplication events per 1,000 residues on average are likely to occur, whereas 10 events of substitution mutation occur. It also is suggested that duplication enhances the probability of occurrence of some peptide motifs, such as those found in zinc fingers and segments with extreme physicochemical characteristics, and, thus, that local repetitiveness is a genomic factor influencing the evolution of eukaryote proteins.     

The influence of nearest-neighboring amino acid residues on aspects of secondary structure of proteins. Attempts to locate -helices and -sheets

The influence of nearest-neighbor pairs of amino acids (n ? 1) and (n + 1) on the conformation of amino acid (n) in proteins has been studied. From experimental data on eleven proteins of known three dimensional structures, our definition of an α-helical domain in the Φ,Ψ plot has been reexamined and found to be satisfactory. On the same principle, a regular β-sheet domain has been delineated. We then revised our 20 × 20 table of frequencies of occurrences of various conformations tabulating three values: α-helical, β-sheet, and neither. These frequencies were then used to locate the helixbreaking positions in cytochrome b₅, papain, thermolysin, and calcium-binding protein. In conjuction with the helical wheel method, they were useful for predicting the locations of most α-helical segments. Similarly the β-sheet breaking positions in papain were located and most of the β-sheets found by X-ray diffraction were close to or between these positions. Data on β-sheets are extremely sparse so that extensive tests were not possible. The application of this method to abnormal hemoglobins suggested possible distortions of helices and in several instances correlated with abnormal properties of the hemoglobins and association with disease. The variable region of human immunoglobin heavy chains was found to have a very low α-helical content though β-sheet structures might exist.     

Pleurocidin-derived antifungal peptides with selective membrane-disruption effect

Pleurocidin (Ple) is a peptide derived from the winter flounder. In our previous study, we reported the antifungal effect of Ple and its mode of action. To develop novel antifungal peptides useful as therapeutic agents, two analogs, with amino acid substitutions, were designed to decrease the net hydrophobicity by Arg (R) or Ser (S)-substitution at the hydrophobic face of Ple without changing the amphipathic structure. By substituting Ser, the hydrophobicity of the peptide (anal-S) was decreased, and by substituting Arg, though the hydrophobicity of the peptide (anal-R) was decreased, the cationicity of this peptide was increased. CD measurements showed the substitution of Arg or Ser decrease the α-helical conformation of analog peptides. Studies with analog peptides have shown decreases in hydrophobicity and α-helicity do not affect antifungal activity but decrease hemolytic activity. These results suggest that highly hydrophobic and α-helical natures are not desirable in the design of antimicrobial peptides.     

Neurexophilin 1 Gene Polymorphism in Chickens and Its Variation Among Species

Neurexophilin 1 (nxph1) has been considered a potential candidate marker for sperm storage in chicken sperm storage tubules. In this work, one mutation of chicken nxph1 was detected. We analyzed 18 nxph1 gene sequences from 18 species. The coding sequence length of the zebra fish nxph1 gene is 819 bp; that of the other species is 816 bp. Amino acid alignment analysis revealed that the gene product is a conserved protein, especially in mammals. The sequences of mammals are highly conserved. We found 202 conserved amino acids (70–271), and there were only eight mutations in the remaining 69 amino acids. That level of conservation could be due to the nxph1 gene having been subjected to substantial constraints or strong purifying selection during millions of years of evolution.     

Probing the stability and mechanism for folding of the GrpE1-112 tetrameric deletion mutant of the GrpE protein from E. coli

Insight into the stability and folding of oligomeric proteins is essential to the understanding of protein folding, especially since the majority of proteins found in nature are oligomeric. A deletion mutant of the GrpE protein from Escherichia coli, that contains the first 112 residues (GrpE1-112) of 197 total, is an oligomeric protein forming a tetrameric structure. A four-helix bundle structure is formed via the interaction of an α-helix (22 amino acids in length) from each monomer. Using both thermal and chemical (urea) denaturation studies, the GrpE1-112 protein has rather low stability with a T(m) of unfolding of 37 °C, a C(m) (urea) of 1.3M, and a ΔG(unfolding) of 8.4 kJ mol(-1). Investigation into the folding pathway using circular dichroism (CD) stopped-flow revealed a two step process with a fast first phase (k(refolding)=8.0 × 10(6)s(-1)M(-1)) forming a multimeric intermediate that possesses significant α-helical content followed by a slow, first order, step forming the folded tetramer.