Fold Surface Research Articles

3D reconstruction of vocal fold dynamics with laser high-speed videoendoscopy in children.

The objective of this study is to evaluate three-dimensional vertical motion of the superior surface of the vocal folds in vivo in (a) typically developing children as a function of vocal frequency variations and (b) a child with vocal nodules. A custom developed laser endoscope coupled with high-speed videoendoscopy was used to obtain 3D parameters from 2 healthy children, one child with vocal nodules, and 23 vocally healthy adults (females = 11, males = 12). Parameters of amplitude (mm), maximum opening/closing velocity (mm/s), and mean opening/closing velocity (mm/s) were computed for the lateral and vertical vibratory motion along the anterior, middle, and posterior sections of the vocal folds were computed. We provide for the first time, absolute measurements of vertical amplitude and maximum/ mean velocity during the opening and closing phases, in vivo in children. Overall, the vertical motion was larger in vocally normal children compared with the lateral motion, especially along the visible posterior section of the vocal folds and during low pitch phonation. The opening phase dynamics were consistently large along the posterior section in the child with vocal nodules. The study findings establish the feasibility of capturing 3D motion in a clinical setting and provide proof of concept for the application of the proposed 3D laser in the pediatric population. Future large sample size studies are needed to establish the diagnostic potential of examining the closing phase vertical motion to evaluate vibratory development in children with normal voice and investigating the opening phase vertical motion in children with nodules. N/A.

Pressure Distributions in Glottal Geometries With Multichannel Airflows

Computer simulation of self-sustained oscillation of the vocal folds has been successful with application of simple Bernoulli-like driving pressures. As voice simulation is now applied to asymmetric vibration with complex mode structures that yield partial vocal fold contact, the driving pressures need refinement. Two independent approaches were used to obtain pressure distributions. The first was a high-fidelity immersed-boundary method computation and the second was a series of pressure tap measurements on scaled-up physical models. Glottal geometries were based on normal surface modes of vibration. Samples are chosen from a large inventory of measured and calculated profiles. Pressure distributions show the complexity that can exist in the driving forces on vocal fold surfaces. Qualitative similarity between computation and measurement was established for a variety of contact patterns, showing diverse pressure gradients in multiple directions. Simplified Bernoulli approaches to glottal pressure distributions are defensible when a single flow channel is preserved in vocal fold oscillation. However, when there are contact islands that produce confluence or difluence of multiple airflow channels, the pressure gradients vary profoundly. Small quantitative differences were observed between measurement and calculation, primarily due to spatial sampling.

Synchronous 3D Imaging of the Medial and Superior Vocal Fold Surface in an excised human Hemilarynx.

This study investigates relationships between the oscillation behavior of the medial and superior vocal fold (VF) surfaces during sustained phonation in a human cadaver hemilarynx. An experimental test stand synchronously captured the medial and superior VF surfaces of a human ex vivo hemilarynx during sustained phonation using two high-speed camera setups in 24 experimental settings. The 3D coordinates of the medial VF surface were reconstructed by triangulation of sewn-in marker points, while laser-based reconstruction was used for the superior VF surface. Correlation analysis and linear regression were used to quantify the connections of the mean and maximal vertical and lateral VF displacements and the VF velocities. Additionally, stepwise linear regression was used to analyze the impact of the measurement variables mean flow rate, adduction and elongation. Strong linear relationships between all of the tested corresponding parameter pairs of the superior and medial VF surfaces were found (p<.001). Mean and maximum vertical displacements of the medial surface were both approximately 50% of the superior surface. The mean lateral displacements for the medial surface were 12% below the superior surface but 12% higher for the maximum values. The mean and maximum VF velocities were 32% and 36% lower for the medial surface. The suggested multi-modal test stand allows efficient, comprehensive analysis of human hemilarynges and provides promising information about the interaction of the different VF areas and opens up the systematic analysis of multiple hemilarynges. In future, our results could integrate into ENT diagnostics using 3D laryngoscopy where the hidden medial VF surface dynamics may be predicted from the observable superior surface.

Formulation and evaluation of bioadhesive buccal Films of Domperidone co-crystals by using Tamarind kernel powder as mucoadhesive polymer

As solubility plays key role in drug dissolution and bioavailability lots of techniques to enhance solubility are evolved. One of the techniques is co crystallization. The main aim of the work is to enhance the solubility of domperidone by co crystallization using coformers like Para amino benzoic acid and succinic acid. The cocrystals were evaluated for melting point and solubility enhancement. these cocrystals were used to prepare buccal films by solvent casting method. In the preparation of buccal films Tamarind kernel powder obtained from the seeds of Tamarind is used as mucoadhesive polymer and Hydroxy propyl methyl cellulose as film former, Polyethylene glycol 6000 as plasticizer, dehydrated banana powder as super disintegrant, sodium saccharin as sweetener and mixture of ethanol and water as solvents. The mucoadhesive strength of Tamarind kernel powder was determined using modified physical balance method. Four buccal films were prepared in which PDBF1 and PDBF2 are the two buccal films prepared using cocrystals of domperidone and Para amino benzoic acid and other two buccal films SDBF1 and SDBF2 with cocrystals of domperidone and Succinic acid. The buccal films were evaluated for different tests like folding endurance, swelling index and Surface pH. In vitro diffusion studies were conducted by Franz diffusion cell using egg membrane as semipermeable membrane and phosphate buffer of pH 7.4. The buccal films prepared with cocrystals of domperidone and succinic acid at weight ratio 1:2 has shown 86%drug release. The work has concluded that there is fold increase in aqueous solubility of Domperidone and the optimized formula is SDBF2 and Tamarind kernel powder can be used as mucoadhesive polymer in novel drug delivery systems. Keywords: co crystals, solvent evaporation, muco adhesive, buccal films, solvent evaporation

A graphical method and workflow for the generation of structure contours for horizontal cylindrical folds

A graphical method developed for the construction of structure contours for inclined planar surfaces has been extended to curved or folded surfaces with cylindrical geometries and horizontal axes. These structure contours can be used to constrain the outcrop trace of a folded contact on a geological map. The extended method requires, as a minimum, a field of orientation data and the map position of a single elevation on the contact under investigation. The method utilises orientation data collected on and around a partially mapped trace of a folded contact to constrain the outcrop trace throughout a geological map. The method uses a vertical cross-section that is parallel to the profile plane of any folds present. Crest, trough and hinge points identified in the cross-section can be projected on to the geological map in their correct positions and elevations. Similarly, structure contours on fold axial surfaces can be projected on to the geological map and the contours used to locate the axial traces of cylindrical folds with horizontal axes.

Hydrolysis of biobased stereocomplex polylactide: Polymorphism dependent crystals degradation and evolution of three-phase crystalline composition

The hydrolytic degradation behavior of stereocomplex polylactide (SCPLA) with distinct polymorphisms (α, αʹ, SC) and SC fractions (the ratio of SC crystallinity to total crystallinity) was first investigated in the present study. The evolution of three-phase crystalline compositions was quantified using modulated differential scanning calorimetry. Hydrolytic degradation commenced in the mobile amorphous fraction (MAF), while both the crystal (CF) and rigid amorphous fraction (RAF) began degradation on Day 3. By the 26th day, the MAF was consumed entirely, followed by the CF and RAF degraded at similar rates, primarily through the cleavage of chains with free ends on the folding surface of the remaining lamella. This work further discussed the influence of polymorphism on homochiral (HC) and SC crystal degradation during hydrolysis. Given racemic helices' participation in SC crystallization, SC-crystal lamellae may possess a higher number of amorphous chains with free ends than HC-crystals. This attribute could account for the faster degradation of HC-crystals in samples with a higher SC fraction.

Indigo Carmine Chromoendoscopy for the Diagnosis of Minor Structural Alterations of the Vocal Fold Cover. A New Application for the Technique

IntroductionMinor structural alterations (MSA) of the laryngeal mucosa are entities involving epithelial vocal cord covering modifications. Among differentiated structural alterations of the vocal cords are sulcus vocalis, epidermoid cysts, micro diaphragms, mucosal bridges, and vasculodysgenesis. While many of these MSA are evident and can be easily visible using conventional endoscopic methods, diagnosis can be difficult even with the help of stroboscopy. MSA can often go unnoticed and may be associated with polyps, cysts or vascular alterations. Its impact on the voice could be significant. In many cases, direct suspension laryngoscopy under general anesthesia is necessary to obtain a definitive diagnosis. ObjectivesThe purpose of this article is to describe a new diagnostic endoscopic method that uses contrast dyes, such as indigo carmine, for the detection of MSA of the vocal fold mucosal covering. Material and MethodsThis research work uses the contrast dye Indigo Carmine as an endoscopic tissue stain, which is applied to the mucosal surface of the vocal cords under local anesthesia in the office or under general anesthesia in the operating room. The dye fills the interstices, highlighting irregularities such as depressions and elevations in architecture. ResultsOur study involved performing indigo carmine chromoendoscopy procedures on patients suspected of having vocal fold MSA type sulcus vocalis, mucosal bridge, or bag type sulcus. We identified cases where this technique is useful for diagnosing previously undetected alterations, shedding light on dysphonia “without an apparent cause”. ConclusionsIndigo carmine chromoendoscopy is a useful technique for detecting minor structural alterations of the mucosal surface of the vocal folds. It has the potential to diagnose MSA in patients where current in-office endoscopic techniques are insufficient.

A CASE REPORT ON THE MANAGEMENT OF SULCUS VOCALIS WITH REFER-ENCE TO SWARASADA

1Sulcus vocalis is a condition characterized by a groove or infolding of the mucosa along the surface of the vocal fold, disrupting the normal physiology of vocal fold vibration and impacting voice production. Common symptoms include hoarseness, vocal fatigue, voice weakness, and increased effort, particularly concerning working professionals who rely on speech for communication and quality of life. While treatment options like phono surgery and speech therapy exist, phono surgery often yields disappointing results, typically limited to increased voice loudness. In Ayurveda, this condition aligns with Swarasada, attributed to factors such as 2Athyucha bhasana(loud speaking) and abhighata(trauma), leading to dosha invasion in sabdhavahi siras and causing speech difficulties. Presented here is a case report involving a 33-year-old IT professional experiencing hoarseness, vocal fatigue, and weakness. Upon bronchoscopy, the diagnosis initially indicated muscle tension dysphonia, later revealing bilateral sulcus vocalis with GERD. The patient underwent Nasya, Gandusha, and Sneha Sweda procedures alongside internal medication. Following a one-month review, the patient exhibited marked improvement in voice clarity. Notably, modern treatments provided only temporary relief. This case report underscores the effective management of sulcus vocalis through Panchakarma treatments and internal medications, showcasing consistent relief over a three-month review period.

Analyzing Vocal Fold Frequency Dynamics Using High-Speed 3D Laser Video Endoscopy.

To examine changes in lateral and vertical vibratory motion along the anterior, middle, and posterior sections of the vocal folds, as a function of vocal frequency variations. Absolute measurements of vocal fold surface dynamics from high-speed videoendoscopy with custom laser endoscope were made on 23 vocally healthy adults during sustained /i:/ production at 10%, 20%, and 80% of pitch range. The 3D parameters of amplitude (mm), maximum velocity opening/closing (mm/s), and mean velocity opening/closing (mm/s) were computed for the lateral and vertical vibratory motion along the anterior, middle, and posterior sections of the vocal folds. Linear mixed model analysis was conducted to evaluate the differences in (a) vocal frequency levels (high vs. normal vs. low pitch), (b) axis level (vertical vs. lateral), (c) position level (anterior vs. middle vs. posterior), and (d) gender differences (male vs. female). Overall, the superior surface vertical motion of the vocal fold is greater compared with the lateral motion, especially in males. Along the superior surface, the mean and maximum closing velocities are greater posteriorly for low pitch. The location (anterior, middle, and posterior) along the superior surface is relevant only for vocal fold closing rather than opening, as the dynamics are different along the various locations. The study highlights the significance of assessing the vertical motion of the superior surface of the vocal fold to understand the complex dynamics of voice production. NA Laryngoscope, 134:3267-3276, 2024.

Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus.

The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.

The underappreciated role of vocal fold medial surface thickness in vocal control

Clinicians and singers are used to viewing vocal fold vibration from a superior endoscopic view. However, both vocal fold vibration and vocal control are three-dimensional. Although it is hidden from the superior view, the vocal fold medial surface shape in the vertical dimension plays an important part in determining both the vibratory pattern as viewed from above and the produced voice.

The Stability and Catastrophic Behavior of Finite Periodic Solutions in Non-Linear Differential Equations

This study focuses on the stability and catastrophic behavior of finite periodic solutions in non-linear differential equations. The occurrence of folding surfaces and their relationship with saddle-node bifurcations are explored, being classified as fold and butterfly types of catastrophes. Additionally, the application of catastrophe theory is discussed to analyze the qualitative changes in solutions with the change in system parameters.

Influence of poly(methyl methacrylate) on the structure and phase transition behavior of poly(vinylidene fluoride)

The structure and organization of poly(vinylidene fluoride) (PVDF) spherulites in blends with poly(methyl methacrylate) of high (PMMA-H) and low (PMMA-L) molecular weights, respectively, have been studied in details. It is confirmed that the addition of PMMA-H and PMMA-L have different influence on the morphologies of PVDF spherulites in several aspects, such as the spacing of ring-band α-PVDF spherulites, the kinetics of both α-PVDF crystallization and α−γ′ solid phase transition, as well as the formation of Wagon-Wheel spherulites. First, incorporation of PMMA-L enlarges the band spacing, which is associated to the increased chain mobility of crystallizable PVDF that helps to release the surface stresses of lamellae. In contrast, the low mobility of PMMA-H chains enhances the congestion at fold surfaces, which results in a vigorous twisting and thus the formation of tightened ring-band α-PVDF structure. Second, the PMMA-H reduces the crystallization rate of PVDF more severely than the PMMA-L, resulting in an extremely slow growth rate of α-PVDF spherulites in PVDF/PMMA-H sample at 160 °C, only about one-twenty-third compared to the neat PVDF. Third, the remarkably reduced α-PVDF spherulite growth rate and enhanced α−γ′ transition rate at 160 °C lead to the formation of Wagon-Wheel PVDF spherulites with inner γ′-PVDF crystals and outer γ crystals. It originates from the synchronization of slow α-PVDF growth and accelerated α−γ′ transition rate through homoepitaxy. That is, when the α−γ′ transition with exceeded rate reaches the growth front of the original α-PVDF spherulite, the transformed γ′-PVDF crystals trigger the growth of γ-PVDF crystals directly from melt with non-band feature. These results help to unravel the formation mechanism of Wagon-Wheel PVDF spherulites to be the competition of α-γ′ crystal transformation and α-spherulite radial growth rates.

Interface instability of the thermal plasma jet

This work is first focused to experimentally study the interface instability and expansion mechanism of thermal plasma jet and provide a better understanding of the complex fluid-dynamic interactions occurring on the surface of the plasma bubble due to the Kelvin–Helmholtz effect. The experimental techniques used include a plasma generator, a pulse-forming network based on the capacitive energy storage, pressure measurement system along the capillary tube, and high-speed camera system to trace the development processes of the plasma interface. Results indicate that the plasmas jet has a better advantage of radial expansion with a high light at the beginning. However, the axial expansion velocity is larger than the radial one with time going on; thus, a torch-shaped jet body occurs under the Rayleigh–Taylor effect and can be divided into two parts including a plasma head and tail. With a dissipation of the initial energy and turbulent mixing between the plasmas and the gas, the jet boundary is broken and even the local rupture phenomena occur on the plasma jet surface. The turbulent dissipation is also very violent when the discharge voltage increases to 3000 V; thus, the turbulent mixing layer between the plasma jet and the gas is quite thicker and the plasma jet boundary is also fuzzy resulting in that the fold surfaces with much larger degree exist earlier. These experimental phenomena are also explained further from the mechanism by deriving the momentum equations of the interface of the plasma jet into the gas. Finally, a fitting formula of the surface area as an important factor in the expansion process of the plasma is obtained to analyze the interface characteristic of the plasma jet.

Stress and strain evolution in fault-related folds: insights from 2D geomechanical modelling

Fault-related folds are intriguing geological structures that develop in compressional and extensional regimes. These folds serve as structural traps for hydrocarbon resources, making their numerical models crucial for understanding the stress and strain evolution of hydrocarbon reservoirs. In our research, we utilize the two-dimensional finite element technique to simulate three representative categories of fault-related folds. Our investigation encompasses their geometric transformation over time, the distribution of stress and strain, variations in slip and uplift, and the effects that various mechanical properties have on these gradients. In our study, we uncovered essential findings about the behavior of fault-related folds. We ascertained that the fault slip gradient in the fault-bend fold model is less than in the fault-propagation fold model. Regarding the uplift gradient, the fault-propagation and fault-bend fold models displayed the greatest and the least degree of change, respectively. The trend of stress-strain evolution on the fold surface in all models was consistent, starting with an increase, transitioning to a constant phase, and ending with a decrease. This pattern proved to be more intricate and divergent than what was evident on the fault surface. Importantly, the internal friction angle, a crucial mechanical characteristic, had a significant influence on the development of these structures. This angle affected both the degree of uplift and stress; an increased angle resulted in enhanced uplift and stress, while a decrease resulted in a decline. Furthermore, the internal friction angle determined the compactness of the fold and the thickness of the forelimb, the part of the fold that inclines towards the advancing direction. These findings have enriched our knowledge of fault-related folds, highlighting the need to consider mechanical properties when studying their formation and evolution.

Polyvinylidene Fluoride (PVDF) Crystallization Kinetics in an Electric Field

To study the effect of applied electric field on polymer crystallization, the crystallization of polyvinylidene fluoride (PVDF) was observed under modified polarized optical microscopy. The PVDF melts were crystallized based on programmed temperature, changes between two transparent conductive glass electrodes, on which a DC electric field was applied. The observations revealed that without the electric field, crystallizations below 160 °C resulted in only α-form crystals, while, at elevated temperatures, the formation of γ-form crystals also occurred. By applying the electric field at 1.7 kV/cm, γ-form crystals started emerging at the slightly lower temperature of 158 °C. Further examinations showed that both crystals, α-form and γ-form, grew at a greater rate with increasing field strength. A careful calculation of the Avrami parameters supported the data that the electric field enhanced the crystallization kinetics. Careful calculation based on the Laurientz–Hoffmann approach revealed that applying the electric field decreased the required energy for PVDF crystallization. The folding surface free energy of the PVDF crystallization, 1.76 × 10−2 Jm−2, was reduced to 1.57 × 10−2 Jm−2 and 1.43 × 10−2 Jm−2 after applying electric fields of 0.8 and 1.7 kVcm−1, respectively. We suggest that the electric field promoted the polymer chain alignment during the crystallization; as a result, it accelerated the polymer crystallization and lowered the energy requirement for crystallization.

Validation and enhancement of a vocal fold medial surface 3D reconstruction approach for in-vivo application

In laryngeal research, studying the vertical vocal fold oscillation component is often disregarded. However, vocal fold oscillation by its nature is a three-dimensional process. In the past, we have developed an in-vivo experimental protocol to reconstruct the full, three-dimensional vocal fold vibration. The goal of this study is to validate this 3D reconstruction method. We present an in-vivo canine hemilarynx setup using high-speed video recording and a right-angle prism for 3D reconstruction of vocal fold medial surface vibrations. The 3D surface is reconstructed from the split image provided by the prism. For validation, reconstruction error was calculated for objects located at a distance of up to 15 mm away from the prism. The influence of camera angle, changing calibrated volume, and calibration errors were determined. Overall average 3D reconstruction error is low and does not exceed 0.12 mm at 5 mm distance from the prism. Influence of a moderate (5°) and large (10°) deviation in camera angle led to a slight increase in error to 0.16 mm and 0.17 mm, respectively. This procedure is robust towards changes in calibration volume and small calibration errors. This makes this 3D reconstruction approach a useful tool for the reconstruction of accessible and moving tissue surfaces.

Super-efficient removal and adsorption mechanism of anionic dyes from water by magnetic amino acid-functionalized diatomite/yttrium alginate hybrid beads as an eco-friendly composite

The development of eco-friendly, large-capacity and easy-to-separate adsorbent materials has always been the focus and difficulty of adsorption technology in wastewater treatment applications based on the characteristics of dye wastewater. Therefore, in this study, a green magnetic glycine(Gly)-functionalized diatomite(Dia)/yttrium alginate (Y-SA) hybrid bead composite (Dia-Gly-Y-SA@Fe3O4) was synthesized by the droplet polymerization, and characterized by various modern analytical techniques. The adsorption performance and adsorption mechanism of the composite were evaluated and elucidated by the removal of anionic dyes direct Blue 106 (DB 106), Congo red (CR) and direct red 13 (DR 13) from water. The results show that the composite is a macroparticle gelpolymer with an average particle size of about 1.5 mm, flower-like fold surface structure, abundant porosity and sensitive magnetic response, and displays ultrastrong adsorption ability for three dyes. The adsorption equilibrium of each dye can be reached quickly within 30 min, and the removal efficiency is more than 95% at pH 2.0 and decreases slightly with pH up to 9.0. The adsorption processes could be explained by the Pseudo-second-order rate equation well. All isotherm data fitted the Langmuir model well, and the maximum adsorption capacities were 1635, 2359 and 1165 mg/g for DB 106, CR and DR 13 at 298 K, respectively. The ultrastrong adsorption performance was due to the multisite interaction of physicochemical action and various hydrogen bonds between hybrid beads and dye anions. As a cost-effective magnetic macroparticle adsorbent prepared by natural ingredients, Dia-Gly-Y-SA@Fe3O4 composite exhibits much more stronger adsorption efficiency, better collectability and no secondary pollution than powder Dia, and would have a good application prospect for the purification of anionic dye wastewater with a wide pH range.

Fold Surfaces of Polymer Crystals Are Nucleation Sites: The Link between Polymer Decoration, Secondary Crystallization, and the Rigid Amorphous Fraction (RAF)

The fold surfaces of polymer crystals may become suitable nucleating sites for uncrystallized material left over during the primary crystallization process. This “nucleation by the folds surface” (NFS) ability is highlighted in the so-called polymer decoration technique in which vapors of polyethylene condense and crystallize on a cold fold surface substrate to form edge-on lamellae that reveal the folds and loops orientations in different growth sectors. In bulk materials, the primary crystallization leaves confined and uncrystallized material between lamellae. NFS, based on epitaxy-type interactions, is expected to take place in these confined and supercooled melt fractions before “true” homogeneous nucleation sets in. The insights provided help elucidate the structural features of the interlamellar layers of crystalline polymers, which overcomes the limits of global, indirect investigation techniques (e.g., differential scanning calorimetry (DSC)) used in attempts to analyze their structure in situ. The interlamellar layer is known to be divided into a rigid amorphous fraction (RAF) located in contact with the fold surfaces and a mobile amorphous fraction (MAF) at its center. The nature of the RAF─amorphous but rigid above its Tg, or crystalline─is still debated. The NFS provides a structural identity for the RAF that associates conformation disorder with stem orientation: the RAF is actually a “condis oriented” fraction. On heating, the small endotherm observed in DSC curves corresponds to its isotropization. The RAF is also a protonucleus for secondary crystallization and induces the growth of edge-on lamellae on top and in the interlamellar spaces of the primary crystals. As such, the RAF has also a layered lamellar structure. Polymer decoration, the “condis oriented” RAF, and the specific edge-on lamellar secondary crystallization are manifestations of the nucleation by the fold surfaces.

Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors

Interleukin-1 receptor-associated kinase 4 (IRAK4) is a vital protein involved in Toll-like and interleukin-1 receptor signal transduction. Several studies have reported regarding the crystal structure, dynamic properties, and interactions with inhibitors of the phosphorylated form of IRAK4. However, no dynamic properties of inhibitor-bound unphosphorylated IRAK4 have been previously studied. Herein, we report the intrinsic dynamics of unphosphorylated IRAK4 (uIRAK4) bound to type I and type II inhibitors. The corresponding apo and inhibitor-bound forms of uIRAK4 were subjected to three independent simulations of 500 ns (total 1.5 μs) each, and their trajectories were analyzed. The results indicated that all three systems were relatively stable, except for the type II inhibitor-bound form of uIRAK4, which exhibited less compact folding and higher solvent surface area. The intra-hydrogen bonds corroborated the structural deformation of the type-II inhibitor-bound complex, which could be attributed to the long molecular structure of the type-II inhibitor. Moreover, the type II inhibitor bound to uIRAK4 showed higher binding free energy with uIRAK4 than the type I inhibitor. The free energy landscape analysis showed a reorientation of Phe330 side chain from the DFG motif at different metastable states for all the systems. The intra-residual distance between residues Lys213, Glu233, Tyr262, and Phe330 suggests a functional interplay when the inhibitors are bound to uIRAK4, thereby hinting at their crucial role in the inhibition mechanism. Ultimately, the intrinsic dynamics study observed between type I/II inhibitor-bound forms of uIRAK4 may assist in better understanding the enzyme and designing therapeutic compounds.