Human hair keratin-associated proteins: Sequence regularities and structural implications

Positions of cysteine residues reveal local clusters and hidden relationships to Sequons and Transmembrane domains in Human proteins

Membrane proteins often possess critical structural features, such as transmembrane domains (TMs), N-glycosylation, and disulfide bonds (SS bonds), which are essential to their structure and function. Here, we extend the study of the motifs carrying N-glycosylation, i.e. the sequons, and the Cys residues supporting the SS bonds, to the whole human proteome with a particular focus on the Cys positions in human proteins with respect to those of sequons and TMs. As the least abundant amino acid residue in protein sequences, the positions of Cys residues in proteins are not random but rather selected through evolution. We discovered that the frequency of Cys residues in proteins is length dependent, and the frequency of CC gaps formed between adjacent Cys residues can be used as a classifier to distinguish proteins with special structures and functions, such as keratin-associated proteins (KAPs), extracellular proteins with EGF-like domains, and nuclear proteins with zinc finger C2H2 domains. Most importantly, by comparing the positions of Cys residues to those of sequons and TMs, we discovered that these structural features can form dense clusters in highly repeated and mutually exclusive modalities in protein sequences. The evolutionary advantages of such complementarity among the three structural features are discussed, particularly in light of structural dynamics in proteins that are lacking from computational predictions. The discoveries made here highlight the sequence-structure-function axis in biological organisms that can be utilized in future protein engineering toward synthetic biology.

Investigating the morphology and genetics of scalp and facial hair characteristics for phenotype prediction

Microscopic traits and ultrastructure of hair such as cross-sectional shape, pigmentation, curvature, and internal structure help determine the level of variations between and across human populations. Apart from cosmetics and anthropological applications, such as determining species, somatic origin (body area), and biogeographic ancestry, the evidential value of hair has increased with rapid progression in the area of forensic DNA phenotyping (FDP). Individuals differ in the features of their scalp hair (greying, shape, colour, balding, thickness, and density) and facial hair (eyebrow thickness, monobrow, and beard thickness) features. Scalp and facial hair characteristics are genetically controlled and lead to visible inter-individual variations within and among populations of various ethnic origins. Hence, these characteristics can be exploited and made more inclusive in FDP, thereby leading to more comprehensive, accurate, and robust prediction models for forensic purposes. The present article focuses on understanding the genetics of scalp and facial hair characteristics with the goal to develop a more inclusive approach to better understand hair biology by integrating hair microscopy with genetics for genotype-phenotype correlation research.

Mapping the Chemistry of Hair Strands by Mass Spectrometry Imaging-A Review

Hair can record chemical information reflecting our living conditions, and, therefore, strands of hair have become a potent analytical target within the biological and forensic sciences. While early efforts focused on analyzing complete hair strands in bulk, high spatial resolution mass spectrometry imaging (MSI) has recently come to the forefront of chemical hair-strand analysis. MSI techniques offer a localized analysis, requiring fewer de-contamination procedures per default and making it possible to map the distribution of analytes on and within individual hair strands. Applying the techniques to hair samples has proven particularly useful in investigations quantifying the exposure to, and uptake of, toxins or drugs. Overall, MSI, combined with optimized sample preparation protocols, has improved precision and accuracy for identifying several elemental and molecular species in single strands of hair. Here, we review different sample preparation protocols and use cases with a view to make the methodology more accessible to researchers outside of the field of forensic science. We conclude that—although some challenges remain, including contamination issues and matrix effects—MSI offers unique opportunities for obtaining highly resolved spatial information of several compounds simultaneously across hair surfaces.

Recent Advances in 3D Printing with Protein-Based Inks

Three-dimensional (3D) printing is a transformative manufacturing strategy, allowing rapid prototyping, customization, and flexible manipulation of structure-property relationships. Proteins are particularly appealing to formulate inks for 3D printing as they serve as essential structural components of living systems, provide a support presence in and around cells and for tissue functions, and also provide the basis for many essential ex vivo secreted structures in nature. Protein-based inks are beneficial in vivo due to their mechanics, chemical and physical match to the specific tissue, and full degradability, while also to promoting implant-host integration and serving as an interface between technology and biology. Exploiting the biological, chemical, and physical features of protein-based inks can provide key opportunities to meet the needs of tissue engineering and regenerative medicine. Despite these benefits, protein-based inks impose nontrivial challenges to 3D printing such as concentration and rheological features and reconstitution of the structural hierarchy observed in nature that is a source of the robust mechanics and functions of these materials. This review introduces photo-crosslinking mechanisms and rheological principles that underpins a variety of 3D printing techniques. The review also highlights recent advances in the design, development, and biomedical utility of monolithic and composite inks from a range of proteins, including collagen, silk, fibrinogen, and others. One particular focus throughout the review is to introduce unique material characteristics of proteins, including amino acid sequences, molecular assembly, and secondary conformations, which are useful for designing printing inks and for controlling the printed structures. Future perspectives of 3D printing with protein-based inks are also provided to support the promising spectrum of biomedical research accessible to these materials.

Keratin intermediate filament chains in tuatara (Sphenodon punctatus): A comparison of tuatara and human sequences

Determination of the sequences of the keratin intermediate filament chains in tuatara has shown that these are closely akin to the α-keratins in human and other vertebrates, especially in the central, coiled-coil rod region. The domain lengths within the rod are preserved exactly, both Type I and Type II chains have been recognised, and sequence identity/homology exists between their respective chains. Nonetheless, there are characteristic differences in amino acid composition and sequence between their respective head (N-terminal) domains and their tail (C-terminal) domains, though some similarities are retained. Further, there is evidence of tandem repeats of a variety of lengths in the tuatara heads and tails indicative of sequence duplication events. These are not evident in human α-keratins and would therefore have implications for the physical attributes of the tissues in the two species. Multiple families of keratin-associated proteins that are ultra-high cysteine-rich or glycine + tyrosine-rich in human and other species do not have direct equivalents in the tuatara. Although high-sulphur proteins are present in tuatara the cysteine residue contents are significantly lower than in human. Further, no sequence homologies between the HS proteins in the two species have been found, thereby casting considerable doubt as to whether any matrix-forming high-sulphur proteins exist in tuatara. These observations may be correlated with the numerous cysteine-rich β-keratins (corneous β-proteins) that are present in tuatara, but which are conspicuously absent in mammals.

Diversity of Trichocyte Keratins and Keratin Associated Proteins

Wool and hair fibres are primarily composed of proteins of which the keratins and keratin associated proteins (KAPs) are the major component. Considerable diversity is known to exist within these two groups of proteins. In the case of the keratins two major families are known, of which there are 11 members in the acidic Type I family and 7 members in the neutral-basic Type II family. The KAPs are even more diverse than the keratins, with 35 families being known to exist when the KAPs found in monotremes, marsupials and other mammalian species are taken into consideration. Human hair and wool are known to have 88 and 73 KAPs respectively, though this number rises for wool when polymorphism within KAP families is included.

Crosslinking Between Trichocyte Keratins and Keratin Associated Proteins

Trichocyte keratins differ considerably from their epithelial cousins in having a higher number of cysteine residues, of which the greater proportion are located in the head and tail regions of these proteins. Coupled with this is the presence of a large number of keratin associated proteins in these fibres that are high in their cysteine content, the high sulfur proteins and ultra-high sulfur proteins. Thus it is the crosslinking that occurs between the cysteines in the keratins and KAPs that is an important determinant in the functionality of wool and hair fibres. Studies have shown the majority of the cysteine residues are involved in internal crosslinking in the KAPs leaving only a few specific cysteines to interact with the keratins, with most evidence pointing to interactions between these KAP cysteines and the keratin head groups.

Chemical Forms of Mercury in Human Hair Reveal Sources of Exposure

Humans are contaminated by mercury in different forms from different sources. In practice, contamination by methylmercury from fish consumption is assessed by measuring hair mercury concentration, whereas exposure to elemental and inorganic mercury from other sources is tested by analysis of blood or urine. Here, we show that diverse sources of hair mercury at concentrations as low as 0.5 ppm can be individually identified by specific coordination to C, N, and S ligands with high energy-resolution X-ray absorption spectroscopy. Methylmercury from seafood, ethylmercury used as a bactericide, inorganic mercury from dental amalgams, and exogenously derived atmospheric mercury bind in distinctive intermolecular configurations to hair proteins, as supported by molecular modeling. A mercury spike located by X-ray nanofluorescence on one hair strand could even be dated to removal of a single dental amalgam. Chemical forms of other known or putative toxic metals in human tissues could be identified by this approach with potential broader applications to forensic, energy, and materials science.

Convergent evolution of cysteine-rich proteins in feathers and hair

Background

Feathers and hair consist of cornified epidermal keratinocytes in which proteins are crosslinked via disulfide bonds between cysteine residues of structural proteins to establish mechanical resilience. Cysteine-rich keratin-associated proteins (KRTAPs) are important components of hair whereas the molecular components of feathers have remained incompletely known. Recently, we have identified a chicken gene, named epidermal differentiation cysteine-rich protein (EDCRP), that encodes a protein with a cysteine content of 36%. Here we have investigated the putative role of EDCRP in the molecular architecture and evolution of feathers.

Results

Comparative genomics showed that the presence of an EDCRP gene and the high cysteine content of the encoded proteins are conserved among birds. Avian EDCRPs contain a species-specific number of sequence repeats with the consensus sequence CCDPCQ(K/Q)(S/P)V, thus resembling mammalian cysteine-rich KRTAPs which also contain sequence repeats of similar sequence. However, differences in gene loci and exon-intron structures suggest that EDCRP and KRTAPs have not evolved from a common gene ancestor but represent the products of convergent sequence evolution. mRNA in situ hybridization demonstrated that chicken EDCRP is expressed in the subperiderm layer of the embryonic epidermis and in the barbule cells of growing feathers. This expression pattern supports the hypothesis that feathers are evolutionarily derived from the subperiderm.

Conclusions

The results of this study suggest that convergent sequence evolution of avian EDCRP and mammalian KRTAPs has contributed to independent evolution of feathers and hair, respectively.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0360-y) contains supplementary material, which is available to authorized users.

Mapping the accessibility of the disulfide crosslink network in the wool fiber cortex

The disulfide bond network within the cortex of mammalian hair has a critical influence on the physical and mechanical characteristics of the fiber. The location, pattern, and accessibility of free and crosslinked cysteines underpin the properties of this network, but have been very difficult to map and understand, because traditional protein extraction techniques require the disruption of these disulfide bonds. Cysteine accessibility in both trichocyte keratins and keratin associated proteins (KAPs) of wool was investigated using staged labeling, where reductants and chaotropic agents were used to expose cysteines in a stepwise fashion according to their accessibility. Cysteines thus exposed were labeled with distinguishable alkylation agents. Proteomic profiling was used to map peptide modifications and thereby explore the role of KAPs in crosslinking keratins. Labeled cysteines from KAPs were detected when wool was extracted with reductant only. Among them were sequences from the end domains of KAPs, indicating that those cysteines were easily accessible in the fiber and could be involved in forming interdisulfide linkages with keratins or with other KAPs. Some of the identified peptides were from the rod domains of Types I and II keratins, with their cysteines positioned on the exposed surface of the α-helix. Peptides were also identified from keratin head and tail domains, demonstrating that they are not buried within the filament structure and, hence, have a possible role in forming disulfide linkages. From this study, a deeper understanding of the accessibility and potential reactivity of cysteine residues in the wool fiber cortex was obtained.

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments

Background

Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.

Results

We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair.

Conclusions

We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.

Expression analysis of KAP9.2 and Hoxc13 genes during different cashmere growth stages by qRT-PCR method

Keratin-associated protein 9.2 (KAP9.2) and Homeobox C13 (Hoxc13) genes were chosen to study because of their biological functions involving hair formation. KAP9.2 gene belongs to the ultra high sulfur KAPs, which is important for hair formation and may have association with cashmere. Hoxc13 takes part in the formation of cashmere keratin and maintaining the normal structure of follicle. It has been reported that Hoxc13 gene exists binding site of KP and KAP genes at its promoter regions in mouse. So the expression of KAP9.2 and Hoxc13 genes was detected at anagen stage vs telogen stage by qRT-PCR. The data showed that KAP9.2 and Hoxc13 gene had similar expression trend at different stages, which indicated that there was interaction between them. KAP9.2 and Hoxc13 gene had lower expression level in anagen than that of in telogen of cashmere growth. In anagen, KAP9.2 and Hoxc13 expressed lower in high cashmere yield individuals than that of in low cashmere yield ones. In telogen, the result was reverse. The study would provide the evidence of involvement of KAP9.2 and Hoxc13 in hair periodic growth.

Fifty years of fibrous protein research: a personal retrospective

As a result of X-ray fiber diffraction studies on fibrous proteins and crystallographic data on fragments derived from them, new experimental techniques across the biophysical and biochemical spectra, sophisticated computer modeling and refinement procedures, widespread use of bioinformatics and improved specimen preparative procedures the structures of many fibrous proteins have now been determined to at least low resolution. In so doing these structures have yielded insight into the relationship that exists between sequence and conformation and this, in turn, has led to improved methodologies for predicting structure from sequence data alone. In this personal retrospective a selection of progress made during the past 50years is discussed in terms of events to which the author has made some contribution.

Fibrous protein nanofibers

One of the promising new techniques in the production of biomaterials is the electrospinning process, whereby fibers of uniform thickness down to the nanoscale can be produced from solutions of polymeric material in a high electric field. At the same time there has been increasing interest in the manufacture of biodegradable nanomaterials from nonfood sources and this has led to investigations into the use of proteins such as collagen, keratin, and fibroin. Explorations into the use of these proteins in the generation of mats suitable for filtration purposes or scaffolds with applications for tissue engineering form the subject of this review.

Keratin-based peptide: biological evaluation and strengthening properties on relaxed hair

A peptide based on a fragment of hair keratin type II cuticular protein, keratin peptide (KP), was studied as a possible strengthening agent for weakened relaxed hair. The peptide was prepared both in aqueous water formulation (WF) and organic solvent formulations (OF), to determine the effect of organic solvents on peptide interaction with hair and the differences in hair recovery. Both peptide formulations were shown to improve mechanical and thermal properties of weakened hair with peptide in OF showing the stronger effect. As a potential new hair care product, and so would necessitate contact with skin, the cytotoxicity and genotoxicity of the peptide were also evaluated through different methodologies (Alamar Blue assay, 2'-7'-dichlorofluorescein probe, cell morphology and growth and evaluation of DNA damage by an alkaline version of the comet assay) in skin fibroblasts. These tests are indicators of the potential of peptide to cause irritation on skin or to be carcinogenic, respectively. The peptide in WF did not cause cytotoxicity or genotoxicity in any of the concentrations tested. The presence of OF, however, induced a 20% decrease in cell viability in all of the range of concentrations used after 72-h incubation. Moreover, OF inhibited cell growth and was considered genotoxic at first contact with cells. The peptide was therefore considered a promising strengthening agent for hair and was shown to be innocuous when applied in WF.

Structure-property relationships of meta-kerateine biomaterials derived from human hair

The structure-property relationships of kerateine materials were studied by separating crude hair extracts into two protein sub-fractions, referred to as α- and γ-kerateines, followed by their de novo recombination into meta-kerateine hydrogels, sponges and films. The kerateine fractions were characterized using electrophoresis and mass spectrometry, which revealed that the α-fraction contained complexes of type I and type II keratins and that the γ-fraction was primarily protein fragments of the α-fraction along with three proteins of the KAP-1 family. Meta-kerateine materials with increased amounts of γ-kerateines showed diminished physical, mechanical and biological characteristics. Most notably, materials with higher γ-content formed less elastic and less solid-like hydrogels and sponges that were less hydrolytically stable. In addition, a model biological assay showed that meta-kerateine films with greater amounts of γ-kerateines were less supportive of hepatocyte attachment. Investigation into the mechanism of attachment revealed that hepatocyte adhesion to meta-kerateines is not mediated by the β1 integrin subunit, despite the presence of LDV binding motifs within the type I α-keratins. This work to define the role of protein composition on biomaterial function is essential for the optimization of keratin biomaterials for biomedical applications.

Proteomic tools for the investigation of human hair structural proteins and evidence of weakness sites on hair keratin coil segments

Human hair is principally composed of hair keratins and keratin-associated proteins (KAPs) that form a complex network giving the hair its rigidity and mechanical properties. However, during their growth, hairs are subject to various treatments that can induce irreversible damage. For a better understanding of the human hair protein structures, proteomic mass spectrometry (MS)-based strategies could assist in characterizing numerous isoforms and posttranslational modifications of human hair fiber proteins. However, due to their physicochemical properties, characterization of human hair proteins using classical proteomic approaches is still a challenge. To address this issue, we have used two complementary approaches to analyze proteins from the human hair cortex. The multidimensional protein identification technology (MudPit) approach allowed identifying all keratins and the major KAPs present in the hair as well as posttranslational modifications in keratins such as cysteine trioxidation, lysine, and histidine methylation. Then two-dimensional gel electrophoresis coupled with MS (2-DE gel MS) allowed us to obtain the most complete 2-DE gel pattern of human hair proteins, revealing an unexpected heterogeneity of keratin structures. Analyses of these structures by differential peptide mapping have brought evidence of cleaved species in hair keratins and suggest a preferential breaking zone in α-helical segments.

Biology of human hair: know your hair to control it

Hair can be engineered at different levels--its structure and surface--through modification of its constituent molecules, in particular proteins, but also the hair follicle (HF) can be genetically altered, in particular with the advent of siRNA-based applications. General aspects of hair biology are reviewed, as well as the most recent contributions to understanding hair pigmentation and the regulation of hair development. Focus will also be placed on the techniques developed specifically for delivering compounds of varying chemical nature to the HF, indicating methods for genetic/biochemical modulation of HF components for the treatment of hair diseases. Finally, hair fiber structure and chemical characteristics will be discussed as targets for keratin surface functionalization.

Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication

Rice plant architecture is an important agronomic trait and a major determinant in high productivity. Panicle erectness is the preferred plant architecture in japonica rice, but the molecular mechanism underlying domestication of the erect panicle remains elusive. Here we report the map-based cloning of a major quantitative trait locus, qPE9-1, which plays an integral role in regulation of rice plant architecture including panicle erectness. The R6547 qPE9-1 gene encodes a 426-amino-acid protein, homologous to the keratin-associated protein 5-4 family. The gene is composed of three Von Willebrand factor type C domains, one transmembrane domain, and one 4-disulfide-core domain. Phenotypic comparisons of a set of near-isogenic lines and transgenic lines reveal that the functional allele (qPE9-1) results in drooping panicles, and the loss-of-function mutation (qpe9-1) leads to more erect panicles. In addition, the qPE9-1 locus regulates panicle and grain length, grain weight, and consequently grain yield. We propose that the panicle erectness trait resulted from a natural random loss-of-function mutation for the qPE9-1 gene and has subsequently been the target of artificial selection during japonica rice breeding.

Expression patterns of keratin intermediate filament and keratin associated protein genes in wool follicles

The catalogue of hair keratin intermediate filaments (KIFs) and keratin-associated proteins (KAPs) present in wool follicles is incomplete. The full coding sequences for three novel sheep KIFs (KRT27, KRT35 and KRT38) and one KAP (KRTAP4-3) were established in this study. Spatial expression patterns of these and other genes (KRT31, KRT85, KRTAP6-1 and trichohyalin) were determined by in situ hybridisation in wool follicles at synchronised stages of growth. Transcription proceeded in the order: trichohyalin, KRT27, KRT85, KRT35, KRT31, KRT38, KRTAP6-1 and KRTAP4-3, as determined by increasing distance of their expression zones from the germinal matrix in anagen follicles. Expression became gradually more restricted to the lower follicle during follicle regression (catagen), and ceased during dormancy (telogen). Some genes (KRT27, KRT31, KRT85 and KRTAP6-1), but not others, were expressed in cortical cells forming the brush-end, indicating specific requirements for the formation of this anchoring structure. The resumption of keratin expression was observed only in later stages of follicle reactivation (proanagen). KIF expression patterns in primary wool follicles showed general resemblance to their human homologues but with some unique features. Consistent differences in localisation between primary and secondary wool follicles were observed. Asymmetrical expression of KRT27, KRT31, KRT35, KRT85 and trichohyalin genes in secondary follicles were associated with bulb deflection and follicle curvature, suggesting a role in the determination of follicle and fibre morphology.

Characterization of Human KAP24.1, A Cuticular Hair Keratin-Associated Protein with Unusual Amino-Acid Composition and Repeat Structure

In a search for genes overexpressed in human sexual hairs, several partial complementary DNA (cDNA) sequences were isolated. Screening of a human scalp cDNA library with one fragment led to the isolation of a full-length cDNA clone, which showed identity to another known sequence, termed KAP24-1 (AB09693). Bioinformatic analysis revealed that the gene for this cDNA consisted of one exon and was located ca. 86 kb away from the chromosome 21q22.1 keratin-associated protein (KAP) gene domain. RT-PCR analysis of a variety of organs showed that KAP24.1 was only present in human scalp. The KAP24.1 protein consisted of 254 amino acids, exhibited a high content of serine, proline, and tyrosine, but low cysteine content and possessed several carboxyterminal tyrosine-containing tandem decameric repeat structures. Evolutionary tree analysis showed no association to other KAP family members. In situ hybridization and indirect immunofluorescence microscopy studies using an antibody derived from KAP24.1 demonstrated specific expression in the middle/upper hair cuticle. The structure of the KRTAP24, its proximity to the chromosome 21q22.1 KAP gene domain, the presence of repeat motifs in the protein and its localization in the hair cuticle points to KAP24.1 being a novel human KAP family member.

Towards a molecular description of intermediate filament structure and assembly

Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central alpha-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.