The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: features of the molecular packing deduced from the sites of induced crosslinks

The susceptibility of disulfide bonds to modification in keratin fibres undergoing tensile stress

Cysteine residues perform a dual role in mammalian hairs. The majority help stabilise the overall assembly of keratins and their associated proteins, but a proportion of inter-molecular disulfide bonds are assumed to be associated with hair mechanical flexibility. Hair cortical microstructure is hierarchical, with a complex macro-molecular organisation resulting in arrays of intermediate filaments at a scale of micrometres. Intermolecular disulfide bonds occur within filaments and between them and the surrounding matrix. Wool fibres provide a good model for studying various contributions of differently situated disulfide bonds to fibre mechanics. Within this context it is not known if all intermolecular disulfide bonds contribute equally, and, if not, then do the disproportionally involved cysteine residues occur at common locations on proteins. In this study, fibres from Romney sheep were subjected to stretching or to breaking point under wet or dry conditions to detect, through labelling, disulfide bonds that were broken more often than randomly. We found that some cysteines were labelled more often than randomly and that these vary with fibre water content (water disrupts protein-protein hydrogen bonds). Many of the identified cysteine residues were located close to the terminal ends of keratins (head or tail domains) and keratin-associated proteins (KAPs). Some cysteines in the head and tail domains of type II keratin K85 were labelled in all experimental conditions. When inter-protein hydrogen bonds were disrupted under wet conditions, disulfide labelling occurred in the head domains of type II keratins, likely affecting keratin-KAP interactions, and tail domains of the type I keratins, likely affecting keratin-keratin interactions. In contrast, in dry fibres (containing more protein-protein hydrogen bonding) disulfide labelling was also observed in the central domains of affected keratins. This central "rod" region is associated with keratin-keratin interactions between anti-parallel heterodimers in the tetramer of the intermediate filament.

Structures of the ß-Keratin Filaments and Keratin Intermediate Filaments in the Epidermal Appendages of Birds and Reptiles (Sauropsids)

The epidermal appendages of birds and reptiles (the sauropsids) include claws, scales, and feathers. Each has specialized physical properties that facilitate movement, thermal insulation, defence mechanisms, and/or the catching of prey. The mechanical attributes of each of these appendages originate from its fibril-matrix texture, where the two filamentous structures present, i.e., the corneous ß-proteins (CBP or ß-keratins) that form 3.4 nm diameter filaments and the α-fibrous molecules that form the 7-10 nm diameter keratin intermediate filaments (KIF), provide much of the required tensile properties. The matrix, which is composed of the terminal domains of the KIF molecules and the proteins of the epidermal differentiation complex (EDC) (and which include the terminal domains of the CBP), provides the appendages, with their ability to resist compression and torsion. Only by knowing the detailed structures of the individual components and the manner in which they interact with one another will a full understanding be gained of the physical properties of the tissues as a whole. Towards that end, newly-derived aspects of the detailed conformations of the two filamentous structures will be discussed and then placed in the context of former knowledge.

Porosity at Different Structural Levels in Human and Yak Belly Hair and Its Effect on Hair Dyeing

Yak belly hair was proposed as a cheap substitute for human hair for the development of hair dyes, as its chemical composition closely resembles human hair in Raman spectroscopy. The absence of melanin in yak belly hair also leads to a strong reduction of fluorescence in Raman measurements, which is advantageous for the investigation of the effectivity of hair dyes. To assess the suitability for replacing human hair, we analyzed similarities and differences of both hair types with a variety of methods: Raman spectroscopy, to obtain molecular information; small-angle X-ray scattering to determine the nanostructure, such as intermediate filament distance, distance of lipid layers and nanoporosity; optical and scanning electron microscopy of surfaces and cross sections to determine the porosity at the microstructural level; and density measurements and tensile tests to determine the macroscopic structure, macroporosity and mechanical properties. Both types of hair are similar on a molecular scale, but differ on other length scales: yak belly hair has a smaller intermediate filament distance on the nanoscale. Most striking is a higher porosity of yak belly hair on all hierarchical levels, and a lower Young’s modulus on the macroscale. In addition to the higher porosity, yak belly hair has fewer overlapping scales of keratin, which further eases the uptake of coloring. This makes, on the other hand, a comparison of coloring processes difficult, and limits the usefulness of yak belly hair as a substitute for human hair.

Structure of intermediate filament assembly in hair deduced from hydration studies using small-angle neutron scattering

Intermediate filaments (IFs) are ubiquitous in biological structures including hair. Small-angle neutron scattering (SANS) data from hydrated samples were used in this study to investigate the distribution of water in hair, and model the structure of the IF assembly. A main diffraction peak at a d-spacing of ∼90 Å, and two weaker reflections show that IFs are arranged in a ∼105 Å quasi-hexagonal lattice. Changes in the diffraction peaks show that only a small fraction of the water absorbed by hair enters between the IFs, and little water diffuses into the core of the IFs. The amount of water in the IF assembly increases rapidly up to 10% relative humidity (RH), and then slowly with further increase in RH. Most of the water appears to reside outside the IF assembly, in the voids and at the interfaces, and contribute to the central diffuse scattering. The IF assembly in the decuticled hair absorbs more water and is more ordered than that the native hair. This suggests that cuticle acts as a barrier, and might constrain the structure by compressing the cortex radially. Treatments with oils that are hydrophobic, heat treatment, and reduction of the S-S linkages that opens up the matrix by disulfide bond cleavage, all affect structure and water permeability. Coconut oil was found to impede hydration more than the soybean oil because of its ability to penetrate deeper into hair. A new model for the IF assembly that is sterically more favorable than the previous models is proposed.

Direct evidence supporting the existence of a helical dislocation in protofilament packing in the intermediate filaments of oxidized trichocyte keratin

The X-ray diffraction patterns of quill and hair, as well as other trichocyte keratin appendages, contain meridional reflections that can be indexed on an axial repeat of 470 Å. Unusually, however, many of the expected orders are not observed. A possible explanation, proposed by Fraser and MacRae (1983), was that the intermediate filaments (IF) that constitute the fibrillar component of the filament/matrix texture consist of 4-chain protofilaments arranged on a surface lattice subject to a helical dislocation. The radial projection of the resulting 8-protofilament ribbon was defined in terms of a two-dimensional unit cell characterized by vectors (a, b) with axial projections z_a ∼ 74 Å and z_b ∼ 198 Å. This situation resembles that found in microtubules, where helical dislocations in subunit packing are also encountered, leading to a so-called "seam" along their length (Metoz and Wade, 1997). In keratin, however, the protofilaments are helical so the seam is inclined to the axis of the IF. Here we report details of the Patterson function that provides independent evidence for both the helical dislocation and the dimensions of the surface lattice. In addition, the observed meridional X-ray amplitudes have been compared with those predicted by various models of the axial distribution of electron density. A new model, adapted from one previously proposed, fits the data significantly better than has heretofore proved possible. An interpretation of the model in terms of either specific keratin-associated-protein (KAP) binding or the retention of IF symmetry by a portion of the head and/or tail domains is suggested.

Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations

Scleroproteins are an important category of proteins within the human body that adopt filamentous, elongated conformations in contrast with typical globular proteins. These include keratin, collagen, and elastin, which often serve a common mechanical function in structural support of cells and tissues. Genetic mutations alter these proteins, disrupting their functions and causing diseases. Computational characterization of these mutations has proven to be extremely valuable in identifying the intricate structure-function relationships of scleroproteins from the molecular scale up, especially if combined with multiscale experimental analysis and the synthesis of model proteins to test specific structure-function relationships. In this work, we review numerous critical diseases that are related to keratin, collagen, and elastin, and through several case studies, we propose ways of extensively utilizing multiscale modeling, from atomistic to coarse-grained molecular dynamics simulations, to uncover the molecular origins for some of these diseases and to aid in the development of novel cures and therapies. As case studies, we examine the effects of the genetic disease Epidermolytic Hyperkeratosis (EHK) on the structure and aggregation of keratins 1 and 10; we propose models to understand the diseases of Osteogenesis Imperfecta (OI) and Alport syndrome (AS) that affect the mechanical and aggregation properties of collagen; and we develop atomistic molecular dynamics and elastic network models of elastin to determine the role of mutations in diseases such as Cutis Laxa and Supravalvular Aortic Stenosis on elastin's structure and molecular conformational motions and implications for assembly.

Structural Hierarchy of Trichocyte Keratin Intermediate Filaments

Although trichocyte keratins (hair, wool, quill, claw) have been studied since the 1930s it is only over the last 30 years or so that major advances have been made in our understanding of the complex structural hierarchy of the filamentous component of this important filament-matrix composite. A variety of techniques, including amino acid sequence analysis, computer modelling, X-ray fibre diffraction and protein crystallography, various forms of electron microscopy, and crosslinking methods have now combined to reveal much of the structural detail. The heterodimeric structure of the keratin molecule is clear, as are the highly-specific modes by which these molecules aggregate to form functionally viable IF. The observation that hair keratin can adopt not one but two structurally-distinct conformations, one formed in the living cells at the base of the hair follicle in a reducing environment and the second in the fully differentiated hair in dead cells in an oxidized state, was unexpected but has major implications for the mechanism of hair growth. Insights have also been made into the mechanism of the uppermost level of hair superstructure, relating to the assembly of the IF in the paracortical and orthocortical macrofibrils.

The structure of the "amorphous" matrix of keratins

Various keratin fibers, particularly human hairs, were investigated by transmission electron microscopy, TEM, solid-state ¹H NMR and Transient Electro-Thermal Technique, TET. The results converge to suggest that the matrix of keratin fiber cortex, far from being amorphous, has a well-defined nano-scale grainy structure, the size of these grains being around 2-4nm. The size of the grains appears to strongly depend on the chemical treatment of the fiber, on the temperature and on the relative humidity of the environment, as well as on the physiological factors at the level of fiber production in follicle. By suggesting an organization at the nano-scale of the protein chains in these grains, likely to be Keratin Associated Proteins, the results challenge the view of matrix as a homogeneous glassy material. Moreover, they indicate the potential of further investigating the purpose of this structure that appears to reflect not only chemical treatments of keratins but also biological processes at the level of the follicle.

Structural Transition of Trichocyte Keratin Intermediate Filaments During Development in the Hair Follicle

The intermediate filaments (IF) in trichocyte (hard α-) keratin are unique amongst the various classes of IF in having not one but two topologically-distinct structures. The first is formed at an early stage of hair development in a reducing environment within the cells in the lower part of the follicle. The second structure occurs at a later stage of hair development in the upper part of the follicle, where there is a transition to an oxidizing environment. Crosslinking studies reveal that molecular slippage occurs within the IF upon oxidation and that this results in many cysteine residues lying in near axial alignment, thereby facilitating disulphide bond formation. The disulphide bonds so formed stabilize the assembly of IF molecules and convert the keratin fibre into a tough, resilient and insoluble structure suitable for its function in vivo as a thermo-regulator and a protector of the animal against its external environment.

Using Data Mining and Computational Approaches to Study Intermediate Filament Structure and Function

Experimental and theoretical research aimed at determining the structure and function of the family of intermediate filament proteins has made significant advances over the past 20 years. Much of this has either contributed to or relied on the amino acid sequence databases that are now available online, and the data mining approaches that have been developed to analyze these sequences. As the quality of sequence data is generally high, it follows that it is the design of the computational and graphical methodologies that are of especial importance to researchers who aspire to gain a greater understanding of those sequence features that specify both function and structural hierarchy. However, these techniques are necessarily subject to limitations and it is important that these be recognized. In addition, no single method is likely to be successful in solving a particular problem, and a coordinated approach using a suite of methods is generally required. A final step in the process involves the interpretation of the results obtained and the construction of a working model or hypothesis that suggests further experimentation. While such methods allow meaningful progress to be made it is still important that the data are interpreted correctly and conservatively. New data mining methods are continually being developed, and it can be expected that even greater understanding of the relationship between structure and function will be gleaned from sequence data in the coming years.

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.

Bidirectional binding property of high glycine-tyrosine keratin-associated protein contributes to the mechanical strength and shape of hair

Since their first finding in wool 50years ago, keratin-associated proteins (KAPs), which are classified into three groups; high sulfur (HS) KAPs, ultra high sulfur (UHS) KAPs, and high glycine-tyrosine (HGT) KAPs, have been the target of curiosity for scientists due to their characteristic amino acid sequences. While HS and UHS KAPs are known to function in disulfide bond crosslinking, the function of HGT KAPs remains unknown. To clarify the function as well as the binding partners of HGT KAPs, we prepared KAP8.1 and other KAP family proteins, the trichocyte intermediate filament proteins (IFP) K85 and K35, the head domain of K85, and the C subdomain of desmoplakin C-terminus (DPCT-C) and investigated the interactions between them in vitro. Western blot analysis and isothermal titration calorimetry (ITC) indicate that KAP8.1 binds to the head domain of K85, which is helically aligned around the axis of the intermediate filament (IF). From these results and transmission electron microscopy (TEM) observations of bundled filament complex in vitro, we propose that the helical arrangement of IFs found in the orthocortex, which is uniquely distributed on the convex fiber side of the hair, is regulated by KAP8.1. Structure-dependent binding of DPCT-C to trichocyte IFP was confirmed by Western blotting, ITC, and circular dichroism. Moreover, DPCT-C also binds to some HGT KAPs. It is probable that such bidirectional binding property of HGT KAPs contribute to the mechanical robustness of hair.

Structure and mechanical properties of human trichocyte keratin intermediate filament protein

Keratin is a protein in the intermediate filament family and the key component of hair, nail, and skin. Here we report a bottom-up atomistic model of the keratin dimer, using the complete human keratin type k35 and k85 amino acid sequence. A detailed analysis of geometric and mechanical properties through full-atomistic simulation with validation against experimental results is presented. We introduce disulfide cross-links in a keratin tetramer and compare the mechanical behavior of the disulfide bonded systems with a system without disulfide bonds. Disulfide bond results in a higher strength (20% increase) and toughness (49% increase), but the system loses α-helical structures under loading, suggesting that disulfide bonds play a significant role in achieving the characteristic mechanical properties of trichocyte α-keratin. Our study provides general insight into the effect of disulfide cross-link on mechanical properties. Moreover, the availability of an atomistic model of this protein opens the possibility to study the mechanical properties of hair fibrils and other fibers from a bottom-up perspective.

Dermatophytes: host-pathogen interaction and antifungal resistance

Cutaneous mycoses are among the most common infections in humans and have become an important public health issue because they cause invasive infections in immunocompromised patients. During the infectious process, dermatophyte-host interactions trigger specific metabolic adaptations that allow the pathogen to adhere to and penetrate the host tissue, scavenge nutrients, and overcome the host defense mechanisms. This metabolic shift and the interplay between metabolism, morphogenesis and stress response are important factors that have been extensively studied in several pathogens. Host cells also respond to the pathogen stimuli by activating intracellular signaling pathways that trigger the immune response against the infectious agent. The comprehension of the molecular aspects of these responses may help to establish new therapeutical strategies. In this review, different aspects of the biology of dermatophytes are addressed, with emphasis on the dermatophyte-host interaction and the mechanisms of antifungal resistance.

Substrate adaptation of Trichophyton rubrum secreted endoproteases

Trichophyton rubrum is the most common pathogen caused the dermatophytosis of nail and skin in human. The secreted proteases were considered to be the most important virulence factors. However, the substrates adaptation of T. rubrum secreted proteases is largely unknown. For the first time, we use the keratins from human nail and skin stratum corneum as the growth medium to investigate the different expression patterns of T. rubrum secreted endoproteases genes. During grow in both keratin-containing media SUB7 and MEP2 were the highest expressed gene in each family. These results indicated that SUB7 and MEP2 may be the dominant endoproteases secreted by T. rubrum during host infection and the other proteases may play a supplementary role. The direct comparison of T. rubrum grown on skin and nail medium showed different substrate favorite of secreted endoproteases. The genes MEP2, SUB5, SUB2 and SUB3 were more active during growth in skin medium, possibly these proteases have a higher affinity for skin original keratins. While the structures of SUB1, SUB4, and MEP4 maybe more suitable for the degradation of nail original keratins. This work presents useful molecular details for further understanding the pathogenesis of secreted proteases and the wide adaptation of T. rubrum.

Describing the structure and assembly of protein filaments by EPR spectroscopy of spin-labeled side chains

In this review we summarize our approach to the study of Intermediate Filament (IF) structure and assembly by electron paramagnetic resonance (EPR) spectroscopy of site-directed spin labels. Using vimentin, a homopolymeric type III IF protein, we demonstrate that this approach serves as a general paradigm for studying protein filament structure and assembly. These strategies will be useful in exploring the structure and assembly properties of other filamentous or aggregation-prone systems.

Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure

alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

Isolation of transcripts over-expressed in human pathogen Trichophyton rubrum during growth in keratin

Trichophyton rubrum is a cosmopolitan and anthropophilic fungus able to invade keratinized tissue, causing infection in human skin and nails. This work evaluated the changes in the extracellular pH during its growth in keratin (after 6, 12, 24, 48, 72h and 7 days) at initial pH 5.0. We observed a gradual increase of basal pH under keratin exposure when compared to glucose condition. Also, we identified 576T. rubrum transcripts differentially expressed by subtractive suppression hybridization (SSH) using conidia cultivated for 72h in keratin as tester, and cultivated in glucose as driver. The over-expression of 238 transcripts obtained under keratin condition was confirmed by macro-array dot-blot, revealing 28 unigenes. Putative proteins encoded by these genes showed similarity to fungi proteins involved in basic metabolism, growth and virulence, i.e., transporters ABC-MDR, MFS and ATPase of copper, NIMA interactive protein, Gag-Pol polyprotein, virulence factors serine-protease subtilisin and metalloprotease, cytochrome P450, GlcN-6-phosphate deaminase and Hsp30. The upregulation of T. rubrum genes encoding subtilisin, metalloprotease and Gag-Pol polyprotein was also validated by northern blot. The results of this study provide the first insight into genes differentially expressed during T. rubrum grown in keratin that may be involved in fungal pathogenesis.

Sequence analyses of Type I and Type II chains in human hair and epithelial keratin intermediate filaments: promiscuous obligate heterodimers, Type II template for molecule formation and a rationale for heterodimer formation

Sequence comparisons have been undertaken for all hair and epithelial keratin IF chains from a single species--human. The results lead to several new proposals. First, it is clear that not only is the chain structure of the molecule an obligate heterodimer but promiscuous association of Type I and Type II chains must occur in vivo. Second, the higher predicted content of alpha-helix in Type II chains in solution relative to that expected for Type I chains suggests that it is the Type II chains that precede their Type I counterparts and that they may serve as templates for molecule formation. Third, heterodimer formation leads naturally to greater structural and functional specificity, and this may be required not only because keratin IF have more interacting partners in its cell type than other types of IF have in theirs but also because hair and skin IF have two distinct structures that relate to the "reducing" or "oxidizing" environment in which they can find themselves. The transition between the two forms may require specific head/tail interactions and this, it is proposed, would be more easily accomplished by a heterodimer structure with its greater in-built specificity.

The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: the nature of the repeating unit

Recently, the spatial distribution of the crosslinks induced between lysine residues in trichocyte (alpha-) keratin intermediate filaments (IF) using disulfosuccinimidyl tartrate was analyzed in detail and the results used to provide information about the three-dimensional structure of the IF [Fraser, R.D.B., Parry, D.A.D., 2005. The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: features of the molecular packing deduced from the sites of induced crosslinks. J. Struct. Biol. 151, 171-181.] The presence of small amounts of 0--> +/-4 crosslinkages between molecular strands four distant in the network implied that the three-dimensional network of interacting molecules must be deeply puckered, but no specific suggestions were made about the nature of the puckering. Whilst it was recognized that there may be more than one type of molecular environment in the structural repeat the initial analysis was confined to the simplest case in which all molecules had the same environment, that is to say the asymmetric unit comprised a single molecule. Further studies reported here suggest that it is likely that the asymmetric unit consists of at least two and possibly as many as four molecules and the implications of this for modeling the structure of trichocyte IF are discussed.