The alpha-helix, an overlooked molecular motor

Biochemical, genomic and structural characteristics of the Acr3 pump in Exiguobacterium strains isolated from arsenic-rich Salar de Huasco sediments

Arsenic is a highly toxic metalloid of major concern for public safety. However, microorganisms have several resistance mechanisms, particularly the expression of arsenic pumps is a critical component for bacterial ability to expel it and decrease intracellular toxicity. In this study, we aimed to characterize the biochemical, structural, and genomic characteristics of the Acr3 pump among a group of Exiguobacterium strains isolated from different sites of the arsenic-rich Salar de Huasco (SH) ecosystem. We also determined whether the differences in As(III) resistance levels presented by the strains could be attributed to changes in the sequence or structure of this protein. In this context, we found that based on acr3 sequences the strains isolated from the SH grouped together phylogenetically, even though clustering based on gene sequence identity did not reflect the strain’s geographical origin. Furthermore, we determined the genetic context of the acr3 sequences and found that there are two versions of the organization of acr3 gene clusters, that do not reflect the strain’s origin nor arsenic resistance level. We also contribute to the knowledge regarding structure of the Acr3 protein and its possible implications on the functionality of the pump, finding that although important and conserved components of this family of proteins are present, there are several changes in the amino acidic sequences that may affect the interactions among amino acids in the 3D model, which in fact are evidenced as changes in the structure and residues contacts. Finally, we demonstrated through heterologous expression that the Exiguobacterium Acr3 pump does indeed improve the organisms As resistance level, as evidenced in the complemented E. coli strains. The understanding of arsenic detoxification processes in prokaryotes has vast biotechnological potential and it can also provide a lot of information to understand the processes of evolutionary adaptation.

Two novel AMHR2 gene variants in monozygotic twins with persistent Müllerian duct syndrome: A case report and functional study

Background

Persistent Müllerian duct syndrome (PMDS) is an autosomal recessive congenital abnormality in which Müllerian derivatives, uterus, cervix, upper two‐thirds of the vagina, and fallopian tubes persist in otherwise normally virilized males. Mutations in anti‐Müllerian hormone (AMH) and AMH receptor type II (AMHR2) genes have been identified as causative. However, functional experimental analysis of AMHR2 or AMH variants that cause PMDS is still lacking.

Materials and Methods

A Chinese Han family affected by PMDS was identified. To assess the history and clinical manifestations of PMDS, physical, operational, ultrasonographical, pathological, and other examinations were performed on family members. The variant screening was conducted using trio whole‐exome sequencing (trio WES) and Sanger sequencing. Complementation‐based NanoLuciferase Binary Technology (NanoBiT) was used to examine the interaction between AMH and AMHR2 variants in vivo. The effect of the two variants on the transcriptional activity of the TGFβ/BMP pathway was evaluated using a luciferase assay.

Results

Classic phenotypic manifestations of PMDS in a pair of identical twins were described and confirmed by genetic sequence analysis. Molecular studies revealed two novel variants c.118G > C [p.(Gly40Arg)], c.1222G > C [p.(Ala408Pro)] in the AMHR2 gene. The AMHR2 p.Gly40Arg variant reduces its ability to bind to AMH, while the p.Ala408Pro variant alters the kinase domain structure. Both variants significantly reduce TGFβ/BMP signaling.

Conclusion

Two missense AMHR2 variants associated with PMDS were identified. These findings provide novel insights toward better clinical evaluation and further understanding of the molecular basis of PMDS.

MAP3K1 Variant Causes Hyperactivation of Wnt4/β-Catenin/FOXL2 Signaling Contributing to 46,XY Disorders/Differences of Sex Development

Background: 46,XY disorders/differences of sex development (46,XY DSD) are congenital conditions that result from abnormal gonadal development (gonadal dysgenesis) or abnormalities in androgen synthesis or action. During early embryonic development, several genes are involved in regulating the initiation and maintenance of testicular or ovarian-specific pathways. Recent reports have shown that MAP3K1 genes mediate the development of the 46,XY DSD, which present as complete or partial gonadal dysgenesis. Previous functional studies have demonstrated that some MAP3K1 variants result in the gain of protein function. However, data on possible mechanisms of MAP3K1 genes in modulating protein functions remain scant.

Methods: This study identified a Han Chinese family with the 46,XY DSD. To assess the history and clinical manifestations for the 46,XY DSD patients, the physical, operational, ultra-sonographical, pathological, and other examinations were performed for family members. Variant analysis was conducted using both trio whole-exome sequencing (trio WES) and Sanger sequencing. On the other hand, we generated transiently transfected testicular teratoma cells (NT2/D1) and ovary-derived granular cells (KGN), with mutant or wild-type MAP3K1 gene. We then performed functional assays such as determination of steady-state levels of gender related factors, protein interaction and luciferase assay system.

Results: Two affected siblings were diagnosed with 46,XY DSD. Our analysis showed a missense c.556A > G/p.R186G variant in the MAP3K1 gene. Functional assays demonstrated that the MAP3K1^R186G variant was associated with significantly decreased affinity to ubiquitin (Ub; 43–49%) and increased affinity to RhoA, which was 3.19 ± 0.18 fold, compared to MAP3K1. The MAP3K1^R186G led to hyperphosphorylation of p38 and GSK3β, and promoted hyperactivation of the Wnt4/β-catenin signaling. In addition, there was increased recruitment of β-catenin into the nucleus, which enhanced the expression of pro-ovarian transcription factor FOXL2 gene, thus contributing to the 46,XY DSD.

Conclusion: Our study identified a missense MAP3K1 variant associated with 46,XY DSD. We demonstrated that MAP3K1^R186G variant enhances binding to the RhoA and improves its own stability, resulting in the activation of the Wnt4/β-catenin/FOXL2 pathway. Taken together, these findings provide novel insights into the molecular mechanisms of 46,XY DSD and promotes better clinical evaluation.

Phosphorylation of myosin regulatory light chain at Ser17 regulates actomyosin dissociation

Phosphorylation of myosin regulatory light chain (MRLC) can regulate muscle contraction and thus affect actomyosin dissociation and meat quality. The objective of this study was to explore the mechanism by how MRLC phosphorylation regulates actomyosin dissociation and thus develop strategies for improving meat quality. Here, the phosphorylation status of MRLC was modulated by myosin light chain kinase and myosin light chain kinase inhibitor. MRLC phosphorylation at Ser17 decreased the kinetic energy and total energy of actomyosin, thus stabilized the structure, facilitating the interaction between myosin and actin; this was one possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation. Moreover, MRLC phosphorylation at Ser17 was beneficial to the formation of ionic bonds, hydrogen bonds, and hydrophobic interaction between myosin and actin, and was the second possible way that MRLC phosphorylation at Ser17 negatively affects actomyosin dissociation.

Advanced Actuator Materials Powered by Biomimetic Helical Fiber Topologies

Helical constructs are ubiquitous in nature at all size domains, from molecular to macroscopic. The helical topology confers unique mechanical functions that activate certain phenomena, such as twining vines and vital cellular functions like the folding and packing of DNA into chromosomes. The understanding of active mechanical processes in plants, certain musculature in animals, and some biochemical processes in cells provides insight into the versatility of the helix. Most of these natural systems consist of helically oriented filaments embedded in a compliant matrix. In some cases, the matrix can change volume and in others the filaments can contract and the matrix is passive. In both cases, the helically arranged fibers determine the overall shape change with a great variety of responses involving length contraction/elongation, twisting, bending, and coiling. Synthetic actuator materials and systems that employ helical topologies have been described recently and demonstrate many fascinating and complex shape changes. However, significant new opportunities exist to mimic some of the most remarkable actions in nature, including the Vorticella's coiling stalk and DNA's supercoils, in the quest for superior artificial muscles.

X-ray Diffraction Studies on the Structural Origin of Dynamic Tension Recovery Following Ramp-Shaped Releases in High-Ca Rigor Muscle Fibers

It is generally believed that during muscle contraction, myosin heads (M) extending from myosin filament attaches to actin filaments (A) to perform power stroke, associated with the reaction, A-M-ADP-Pi → A-M + ADP + Pi, so that myosin heads pass through the state of A-M, i.e., rigor A-M complex. We have, however, recently found that: (1) an antibody to myosin head, completely covering actin-binding sites in myosin head, has no effect on Ca²⁺-activated tension in skinned muscle fibers; (2) skinned fibers exhibit distinct tension recovery following ramp-shaped releases (amplitude, 0.5% of Lo; complete in 5 ms); and (3) EDTA, chelating Mg ions, eliminate the tension recovery in low-Ca rigor fibers but not in high-Ca rigor fibers. These results suggest that A-M-ADP myosin heads in high-Ca rigor fibers have dynamic properties to produce the tension recovery following ramp-shaped releases, and that myosin heads do not pass through rigor A-M complex configuration during muscle contraction. To obtain information about the structural changes in A-M-ADP myosin heads during the tension recovery, we performed X-ray diffraction studies on high-Ca rigor skinned fibers subjected to ramp-shaped releases. X-ray diffraction patterns of the fibers were recorded before and after application of ramp-shaped releases. The results obtained indicate that during the initial drop in rigor tension coincident with the applied release, rigor myosin heads take up applied displacement by tilting from oblique to perpendicular configuration to myofilaments, and after the release myosin heads appear to rotate around the helical structure of actin filaments to produce the tension recovery.

Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches

Background

Previously, the hypothetical protein, KPN00728 from Klebsiella pneumoniae MGH78578 was the Succinate dehydrogenase (SDH) chain C subunit via structural prediction and molecular docking simulation studies. However, due to limitation in docking simulation, an in-depth understanding of how SDH interaction occurs across the transmembrane of mitochondria could not be provided.

Results

In this present study, molecular dynamics (MD) simulation of KPN00728 and SDH chain D in a membrane was performed in order to gain a deeper insight into its molecular role as SDH. Structural stability was successfully obtained in the calculation for area per lipid, tail order parameter, thickness of lipid and secondary structural properties. Interestingly, water molecules were found to be highly possible in mediating the interaction between Ubiquinone (UQ) and SDH chain C via interaction with Ser27 and Arg31 residues as compared with earlier docking study. Polar residues such as Asp95 and Glu101 (KPN00728), Asp15 and Glu78 (SDH chain D) might have contributed in the creation of a polar environment which is essential for electron transport chain in Krebs cycle.

Conclusions

As a conclusion, a part from the structural stability comparability, the dynamic of the interacting residues and hydrogen bonding analysis had further proved that the interaction of KPN00728 as SDH is preserved and well agreed with our postulation earlier.

The different muscle-energetics during shortening and stretch

The helical shape of the thin filaments causes their passive counterclockwise rotation during muscle stretch that increases tensile stress and torque at first by unwinding and then by winding up the four anchoring Z-filaments. This means storage of energy in the series elastic Z-filaments and a considerable decrease of the liberated energy of heat and work to (h-w(ap)), where h is the heat energy and w(ap) the stretch energy induced from outside by an apparatus. The steep thin filament helix with an inclination angle of 70° promotes the passive rotation during stretch, but impedes the smooth sliding of shortening by increased friction and production of frictional heat. The frictional heat may be produced by the contact with the myosin cross-bridges: (1) when they passively snap on drilling thin filaments from cleft to cleft over a distance 2 × 2.7 nm = 5.4 nm between the globular actin monomers in one groove, causing stepwise motion; or (2) when they passively cycle from one helical groove to the next (distance 36 nm). The latter causes more heat and may take place on rotating thin filaments without an effective forward drilling ("idle rotation"), e.g., when they produce "unexplained heat" at the beginning of an isometric tetanus. In an Appendix to this paper the different states of muscle are defined. The function of its most important components is described and rotation model and power-stroke model of muscular contraction is compared.

Large-scale models reveal the two-component mechanics of striated muscle

This paper provides a comprehensive explanation of striated muscle mechanics and contraction on the basis of filament rotations. Helical proteins, particularly the coiled-coils of tropomyosin, myosin and alpha-actinin, shorten their H-bonds cooperatively and produce torque and filament rotations when the Coulombic net-charge repulsion of their highly charged side-chains is diminished by interaction with ions. The classical "two-component model" of active muscle differentiated a "contractile component" which stretches the "series elastic component" during force production. The contractile components are the helically shaped thin filaments of muscle that shorten the sarcomeres by clockwise drilling into the myosin cross-bridges with torque decrease (= force-deficit). Muscle stretch means drawing out the thin filament helices off the cross-bridges under passive counterclockwise rotation with torque increase (= stretch activation). Since each thin filament is anchored by four elastic alpha-actinin Z-filaments (provided with force-regulating sites for Ca(2+) binding), the thin filament rotations change the torsional twist of the four Z-filaments as the "series elastic components". Large scale models simulate the changes of structure and force in the Z-band by the different Z-filament twisting stages A, B, C, D, E, F and G. Stage D corresponds to the isometric state. The basic phenomena of muscle physiology, i. e. latency relaxation, Fenn-effect, the force-velocity relation, the length-tension relation, unexplained energy, shortening heat, the Huxley-Simmons phases, etc. are explained and interpreted with the help of the model experiments.

"Hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms

Background

A wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. These include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. It has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. In this work, protein crystal structures from hyper/thermophilic organisms and their mesophilic homologs have been compared, in order to quantify the difference of apolar contact area and to assess the role played by the hydrophobic contacts in the stabilization of the protein core, at high temperatures.

Results

The construction of two datasets was carried out so as to satisfy several restrictive criteria, such as minimum redundancy, resolution and R-value thresholds and lack of any structural defect in the collected structures. This approach allowed to quantify with relatively high precision the apolar contact area between interacting residues, reducing the uncertainty due to the position of atoms in the crystal structures, the redundancy of data and the size of the dataset. To identify the common core regions of these proteins, the study was focused on segments that conserve a similar main chain conformation in the structures analyzed, excluding the intervening regions whose structure differs markedly. The results indicated that hyperthermophilic proteins underwent a significant increase of the hydrophobic contact area contributed by those residues composing the alpha-helices of the structurally conserved regions.

Conclusion

This study indicates the decreased flexibility of alpha-helices in proteins core as a major factor contributing to the enhanced termostability of a number of hyperthermophilic proteins. This effect, in turn, may be due to an increased number of buried methyl groups in the protein core and/or a better packing of alpha-helices with the rest of the structure, caused by the presence of hydrophobic beta-branched side chains.

Actin immobilization on chitin for purifying myosin II: A laboratory exercise that integrates concepts of molecular cell biology and protein chemistry

This article presents our experience on teaching biochemical sciences through an innovative approach that integrates concepts of molecular cell biology and protein chemistry. This original laboratory exercise is based on the preparation of an affinity chromatography column containing F-actin molecules immobilized on chitin particles for purifying skeletal myosin II. It favors the active learning of protein extraction and purification, the learning of concepts such as muscle contraction, cytoskeleton structure, and its importance for the living cell. This laboratory exercise also promotes learning biotechnological applications of chitin and the applications of protein immobilization in different industrial fields. Furthermore, the activities target the development of laboratorial abilities, problem-solving skills, and the ability to write a scientific report, following the model of a scientific article. The trials are mainly proposed for either an undergraduate project for advanced students in the life sciences or a postgraduate practical training course. In both the cases, the students must have had biochemistry as part of their regular curriculum. Alternatively, the affinity chromatography method can fit in any regular biochemistry course if active chitin, F-actin, and a myosin II extract are provided. It is very important to mention that this laboratory exercise can be used even in places where a facility such as ultracentrifugation is lacking. For that, the steps of actin purification are skipped, and actin is commercially obtained. Therefore, it is an adequate approach for the active learning of biochemical and molecular cell biology principles and techniques even in poor countries.