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Showing papers in "Progress in Biophysics & Molecular Biology in 2017"


Journal ArticleDOI
TL;DR: Bacterial lipases have been extensively studied during last decade, however, their wider applications demand a detailed review on purification, catalytic characterization and applications of lipases.
Abstract: Lipase (E.C.3.1.1.3) belongs to the hydrolases and is also known as fat splitting, glycerol ester hydrolase or triacylglycerol acylhydrolase. Lipase catalyzes the hydrolysis of triglycerides converting them to glycerol and fatty acids in an oil-water interface. These are widely used in food, dairy, flavor, pharmaceuticals, biofuels, leather, cosmetics, detergent, and chemical industries. Lipases are of plant, animal, and microbial origin, but microbial lipases are produced at industrial level and represent the most widely used class of enzymes in biotechnological applications and organic chemistry. Phylogenetic analysis and comparison of residues around GxSxG motif provided an insight to the diversity among bacterial lipases. A variety of para-Nitrophenyl (p-NP) esters having C2 to C16 (p-NP acetate to p-NP palmitate) in their fatty acid side chain can be hydrolyzed by bacterial lipases. Large heterogeneity has been observed in molecular and catalytic characteristics of lipases including molecular mass; 19–96 kDa, Km; 0.0064–16.58 mM, Kcat; 0.1665–1.0 × 104 s−1 and Kcat/Km; 26.02–7377 s-1/mM. Optimal conditions of their working temperature and pH have been stated 15–70 °C and 5.0–10.8, respectively and are strongly associated with the type and growth conditions of bacteria. Surface hydrophobicity, enzyme activity, stability in organic solvents and at high temperature, proteolytic resistance and substrate tolerance are the properties of bacterial lipases that have been improved by engineering. Bacterial lipases have been extensively studied during last decade. However, their wider applications demand a detailed review on purification, catalytic characterization and applications of lipases.

197 citations


Journal ArticleDOI
TL;DR: It is proposed that a better understanding of how mutations affect the structure, function, and formation of multiprotein complexes provides novel opportunities for tackling mutations, including the development of small-molecule drugs targeted specifically to mutated PPIs.
Abstract: Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance. The importance of these protein mutations has led to the development of many resources for understanding and predicting their effects. We propose that a better understanding of how these mutations affect the structure, function, and formation of multiprotein complexes provides novel opportunities for tackling them, including the development of small-molecule drugs targeted specifically to mutated PPIs.

132 citations


Journal ArticleDOI
TL;DR: It is developed the idea, and the evidence is summarized, that in many cases the anomalous fibrin fibre formation seen in such diseases actually amounts to amyloidogenesis.
Abstract: The chief and largely terminal element of normal blood clotting is considered to involve the polymerisation of the mainly α-helical fibrinogen to fibrin, with a binding mechanism involving ‘knobs and holes’ but with otherwise little change in protein secondary structure. We recognise, however, that extremely unusual mutations or mechanical stressing can cause fibrinogen to adopt a conformation containing extensive β-sheets. Similarly, prions can change morphology from a largely α-helical to largely β-sheet conformation, and the latter catalyses both the transition and the self-organising polymerisation of the β-sheet structures. Many other proteins can also do this, where it is known as amyloidogenesis. When fibrin is formed in samples from patients harbouring different diseases it can have widely varying diameters and morphologies. We here develop the idea, and summarise the evidence, that in many cases the anomalous fibrin fibre formation seen in such diseases actually amounts to amyloidogenesis. In particular, fibrin can interact with the amyloid-β (Aβ) protein that is misfolded in Alzheimer's disease. Seeing these unusual fibrin morphologies as true amyloids explains a great deal about fibrin(ogen) biology that was previously opaque, and provides novel strategies for treating such coagulopathies. The literature on blood clotting can usefully both inform and be informed by that on prions and on the many other widely recognised (β-)amyloid proteins. A preprint has been lodged in bioRxiv (Kell and Pretorius, 2016).

71 citations


Journal ArticleDOI
TL;DR: Evaluating the effect of extracellular potassium concentration and activation of the ATP-sensitive inward-rectifying potassium current on action potential duration, post-repolarization refractoriness, and conduction velocity, as the most critical factors in determining reentry vulnerability during ischemia shows that the Grandi and O'Hara models required modifications to reproduce expected ischemic changes.
Abstract: Acute myocardial ischemia is one of the main causes of sudden cardiac death. The mechanisms have been investigated primarily in experimental and computational studies using different animal species, but human studies remain scarce. In this study, we assess the ability of four human ventricular action potential models (ten Tusscher and Panfilov, 2006; Grandi et al., 2010; Carro et al., 2011; O'Hara et al., 2011) to simulate key electrophysiological consequences of acute myocardial ischemia in single cell and tissue simulations. We specifically focus on evaluating the effect of extracellular potassium concentration and activation of the ATP-sensitive inward-rectifying potassium current on action potential duration, post-repolarization refractoriness, and conduction velocity, as the most critical factors in determining reentry vulnerability during ischemia. Our results show that the Grandi and O'Hara models required modifications to reproduce expected ischemic changes, specifically modifying the intracellular potassium concentration in the Grandi model and the sodium current in the O'Hara model. With these modifications, the four human ventricular cell AP models analyzed in this study reproduce the electrophysiological alterations in repolarization, refractoriness, and conduction velocity caused by acute myocardial ischemia. However, quantitative differences are observed between the models and overall, the ten Tusscher and modified O'Hara models show closest agreement to experimental data.

58 citations


Journal ArticleDOI
TL;DR: A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions and does this by binding, via PXXP motifs, to the OB-fold of a nearby protein.
Abstract: The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions. It does this by binding, via PXXP motifs, to the OB-fold (aka SH3 domain) of a nearby protein. When the nearby protein is another SSB tetramer, this leads to a highly efficient ssDNA binding reaction that rapidly and cooperatively covers and protects the exposed nucleic acid from degradation. Alternatively, when the nearby protein is a member of the SSB interactome, loading of the enzyme onto the DNA takes places.

55 citations


Journal ArticleDOI
TL;DR: Evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.
Abstract: An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.

54 citations


Journal ArticleDOI
TL;DR: A 3 × 3 matrix has been proposed to allow computational biology models to be categorised with respect to their testability and epistemic foundation in order to guide the selection of an appropriate process of validation to supply evidence to establish credibility.
Abstract: Computational models in biology and biomedical science are often constructed to aid people's understanding of phenomena or to inform decisions with socioeconomic consequences. Model credibility is the willingness of people to trust a model's predictions and is often difficult to establish for computational biology models. A 3 × 3 matrix has been proposed to allow such models to be categorised with respect to their testability and epistemic foundation in order to guide the selection of an appropriate process of validation to supply evidence to establish credibility. Three approaches to validation are identified that can be deployed depending on whether a model is deemed untestable, testable or lies somewhere in between. In the latter two cases, the validation process involves the quantification of uncertainty which is a key output. The issues arising due to the complexity and inherent variability of biological systems are discussed and the creation of ‘digital twins’ proposed as a means to alleviate the issues and provide a more robust, transparent and traceable route to model credibility and acceptance.

50 citations


Journal ArticleDOI
TL;DR: The present study adjusted critical parameters to optimize a regimen for hiPSC-CM transformation, which will open up new avenues for electro-mechanical stimulation by allowing temporal and spatial control of stimuli which can be easily scaled up in complexity for cardiac development and disease modelling.
Abstract: Rationale Impaired maturation of human iPSC-derived cardiomyocytes (hiPSC-CMs) currently limits their use in experimental research and further optimization is required to unlock their full potential. Objective To push hiPSC-CMs towards maturation, we recapitulated the intrinsic cardiac properties by electro-mechanical stimulation and explored how these mimetic biophysical cues interplay and influence the cell behaviour. Methods and results We introduced a novel device capable of applying synchronized electrical and mechanical stimuli to hiPSC-CM monolayers cultured on a PDMS membrane and evaluated effects of conditioning on cardiomyocyte structure and function. Human iPSC-CMs retained their cardiac phenotype and displayed adaptive structural responses to electrical (E), mechanical (M) and combined electro-mechanical (EM) stimuli, including enhanced membrane N-cadherin signal, stress-fiber formation and sarcomeric length shortening, most prominent under the EM stimulation. On the functional level, EM conditioning significantly reduced the transmembrane calcium current, resulting in a shift towards triangulation of intracellular calcium transients. In contrast, E and M stimulation applied independently increased the proportion of cells with L-Type calcium currents. In addition, calcium transients measured in the M-conditioned samples advanced to a more rectangular shape. Conclusion The new methodology is a simple and elegant technique to systematically investigate and manipulate cardiomyocyte remodelling for translational applications. In the present study, we adjusted critical parameters to optimize a regimen for hiPSC-CM transformation. In the future, this technology will open up new avenues for electro-mechanical stimulation by allowing temporal and spatial control of stimuli which can be easily scaled up in complexity for cardiac development and disease modelling.

50 citations


Journal ArticleDOI
TL;DR: The current knowledge regarding the role of immune cells in bone remodelling, and its implications in emerging basic and clinical investigations into the pathogenesis and management of subchondral bone pathologies in OA are discussed.
Abstract: Osteoarthritis (OA) is a whole-joint disorder, and non-cartilage articular pathologies, e.g. subchondral bone disturbance, contribute substantially to the onset and progression of the disease. In the early stage of OA, abnormal mechanical loading leads to micro-cracks or micro-fractures that trigger a reparative process with angiogenesis and inflammatory response. With the progression of disease, cystic lesion, sclerosis and osteophytosis occur at tissue level, and osteoblast dysfunction at cellular level. Osteoblasts derived from OA sclerotic bone produce increased amount of type I collagen with aberrant Col1A1/A2 ratio and poor mineralization capability. The coupling mechanism of bone resorption with formation is also impaired with elevated osteoclastic activities. All these suggest a view that OA subchondral bone presents a defective fracture repair process in a chronic course. It has been found that T and B cells, the major effectors in the adaptive immunity, take part in the hard callus formation at fracture site in addition to the initial phase of haematoma and inflammation. Infiltration of lymphocytes could interplay with osteoclasts and osteoblasts via a direct physical cell-to-cell contact. Several lines of evidence have consistently shown the involvement of T and B cells in osteoclastogenesis and bone erosion in arthritic joints. Yet the biological link between immune cells and osteoblastic function remains ambiguous. This review will discuss the current knowledge regarding the role of immune cells in bone remodelling, and address its implications in emerging basic and clinical investigations into the pathogenesis and management of subchondral bone pathologies in OA.

47 citations


Journal ArticleDOI
TL;DR: It is presented that cellular life and evolutionary development are a self-organizing cellular response to uncertainty in iterative conformity with its basal initiating parameters, and permits a reasoned unification between Western rational reductionism and Eastern holism.
Abstract: Boundary conditions enable cellular life through negentropy, chemiosmosis, and homeostasis as identifiable First Principles of Physiology. Self-referential awareness of status arises from this organized state to sustain homeostatic imperatives. Preferred homeostatic status is dependent upon the appraisal of information and its communication. However, among living entities, sources of information and their dissemination are always imprecise. Consequently, living systems exist within an innate state of ambiguity. It is presented that cellular life and evolutionary development are a self-organizing cellular response to uncertainty in iterative conformity with its basal initiating parameters. Viewing the life circumstance in this manner permits a reasoned unification between Western rational reductionism and Eastern holism.

47 citations


Journal ArticleDOI
TL;DR: Experimental evidence is overviewed of the involvement of TRPC3 and TRPC6 in cardiac physiology and pathophysiology in response to stretch that contributes to the physiological stretch-induced slow force response (SFR).
Abstract: Transient receptor potential (TRP) channels constitute a large family of versatile multi-signal transducers. In particular, TRP canonical (TRPC) channels are known as receptor-operated, non-selective cation channels. TRPC3 and TRPC6, two members in the TRPC family, are highly expressed in the heart, and participate in the pathogenesis of cardiac hypertrophy and heart failure as a pathological response to chronic mechanical stress. In the pathological response, myocardial stretch increases intracellular Ca2+ levels and activates nuclear factor of activated T cells to induce cardiac hypertrophy. Recent studies have revealed that TRPC3 and TRPC6 also contribute to the physiological stretch-induced slow force response (SFR), a slow increase in the Ca2+ transient and twitch force during stretch. In the physiological response, a stretch-induced increase in intracellular Ca2+ mediated by TRPC3 and TRPC6 causes the SFR. We here overview experimental evidence of the involvement of TRPC3 and TRPC6 in cardiac physiology and pathophysiology in response to stretch.

Journal ArticleDOI
TL;DR: Questions remain regarding Piezo's role in muscle function due to the non-selective nature of GsMTx4 inhibition toward membrane mechanoenzymes and the implication of MCS channel types by genetic knockdown, but evidence supporting Piezo like activity, at least in the developmental stages of muscle, is presented.
Abstract: Discovery of Piezo channels and the reporting of their sensitivity to the inhibitor GsMTx4 were important milestones in the study of non-selective cationic mechanosensitive channels (MSCs) in normal physiology and pathogenesis. GsMTx4 had been used for years to investigate the functional role of cationic MSCs, especially in muscle tissue, but with little understanding of its target or inhibitory mechanism. The sensitivity of Piezo channels to bilayer stress and its robust mechanosensitivity when expressed in heterologous systems were keys to determining GsMTx4's mechanism of action. However, questions remain regarding Piezo's role in muscle function due to the non-selective nature of GsMTx4 inhibition toward membrane mechanoenzymes and the implication of MCS channel types by genetic knockdown. Evidence supporting Piezo like activity, at least in the developmental stages of muscle, is presented. While the MSC targets of GsMTx4 in muscle pathology are unclear, its muscle protective effects are clearly demonstrated in two recent in situ studies on normal cardiomyocytes and dystrophic skeletal muscle. The muscle protective function may be due to the combined effect of GsMTx4's inhibitory action on cationic MSCs like Piezo and TRP, and its potentiation of repolarizing K+ selective MSCs like K2P and SAKCa. Paradoxically, the potent in vitro action of GsMTx4 on many physiological functions seems to conflict with its lack of in situ side-effects on normal animal physiology. Future investigations into cytoskeletal control of sarcolemma mechanics and the suspected inclusion of MSCs in membrane micro/nano sized domains with distinct mechanical properties will aide our understanding of this dichotomy.

Journal ArticleDOI
TL;DR: This review presents structural and biochemical work that has unveiled novel interaction interfaces on FHA domains and discusses how these non-canonical interactions modulate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization - events that collectively determine FHA function.
Abstract: Forkhead-associated (FHA) domains are small phosphopeptide recognition modules found in eubacterial and eukaryotic, but not archeal, genomes. Although they were originally found in forkhead-type transcription factors, they have now been identified in many other signaling proteins. FHA domains share a remarkably conserved fold despite very low sequence conservation. They only have five conserved amino acids that are important for binding to phosphorylated epitopes. Recent work from several laboratories has demonstrated that FHA domains can mediate many interactions that do not depend on their ability to recognize a phosphorylated threonine. In this review, we present structural and biochemical work that has unveiled novel interaction interfaces on FHA domains. We discuss how these non-canonical interactions modulate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization - events that collectively determine FHA function.

Journal ArticleDOI
TL;DR: It is concluded that the principle of optimality in biology is related to the establishment of spatiotemporal patterns that are maximally predictable and can hold the living state for a prolonged time by the selection of a habitable space approximated to the conditions described by classical physics.
Abstract: Living systems inhabit the area of the world which is shaped by the predictable space-time of physical objects and forces that can be incorporated into their perception pattern. The process of selecting a "habitable" space-time is the internal quantum measurement in which living systems become embedded into the environment that supports their living state. This means that living organisms choose a coordinate system in which the influence of measurement is minimal. We discuss specific roles of biological macromolecules, in particular of the cytoskeleton, in shaping perception patterns formed in the internal measurement process. Operation of neuron is based on the transmission of signals via cytoskeleton where the digital output is generated that can be decoded through a reflective action of the perceiving agent. It is concluded that the principle of optimality in biology as formulated by Liberman et al. (BioSystems 22, 135-154, 1989) is related to the establishment of spatiotemporal patterns that are maximally predictable and can hold the living state for a prolonged time. This is achieved by the selection of a habitable space approximated to the conditions described by classical physics.

Journal ArticleDOI
TL;DR: It is argued here that the essential processes of cognition, response and decision-making inherent in living cells transcend conventional modelling, and microscopic studies of organisms reveal a level of cellular intelligence that is unrecognized by science and is not amenable to computer analysis.
Abstract: Traditions of Eastern thought conceptualised life in a holistic sense, emphasising the processes of maintaining health and conquering sickness as manifestations of an essentially spiritual principle that was of overriding importance in the conduct of living. Western science, which drove the overriding and partial eclipse of Eastern traditions, became founded on a reductionist quest for ultimate realities which, in the modern scientific world, has embraced the notion that every living process can be successfully modelled by a digital computer system. It is argued here that the essential processes of cognition, response and decision-making inherent in living cells transcend conventional modelling, and microscopic studies of organisms like the shell-building amoebae and the rhodophyte alga Antithamnion reveal a level of cellular intelligence that is unrecognized by science and is not amenable to computer analysis.

Journal ArticleDOI
TL;DR: Investigating the interactions of MEF2C and its directly-interacting proteins is not only helpful to understand of the physiological function of MEf2C, but also provides a target for future rational drug design.
Abstract: Myocyte enhancer factor 2C (MEF2C) is a transcription factor of MADS box family involved in the early development of several human cells including muscle (i.e., skeletal, cardiac, and smooth), neural, chondroid, immune, and endothelial cells. Dysfunction of MEF2C leads to embryo hypoplasia, disorganized myofibers and perinatal lethality. The main role of MEF2C is its regulation of muscle development. It has been reported that MEF2C-knockout mice die on embryonic day 9.5 from unnatural development of cardiovascular. The effects of MEF2C are mediated by its directly-interacting proteins; therefore, the investigation of these interactions is critical in order to clarify MEF2C's biological function. In this study, we review twenty-five proteins that directly interact with MEF2C, including nineteen proteins related to muscle development, four proteins related to neural cell development, one protein related to chondroid cell development, four proteins related to immune cell development, and two proteins related to endothelial cell development. Among these proteins, the interaction of MEF2C with MRFs is important for differentiation of developing muscle cells. MEF2C interacts with Sox18 for endothelial vessel morphogenesis. The interaction of MEF2C with Cabin1 is important for maintaining T-cell inactivation. Investigating the interactions of MEF2C and its directly-interacting proteins is not only helpful to understand of the physiological function of MEF2C, but also provides a target for future rational drug design.

Journal ArticleDOI
TL;DR: It is shown how evolutionary relations between protein functional superfamilies and folds delineated with the help of EFLs can contribute to establishing the rules for design of desired enzymatic functions.
Abstract: Study of the hierarchy of domain structure with alternative sets of domains and analysis of discontinuous domains, consisting of remote segments of the polypeptide chain, raised a question about the minimal structural unit of the protein domain. The hypothesis on the decisive role of the polypeptide backbone in determining the elementary units of globular proteins have led to the discovery of closed loops. It is reviewed here how closed loops form the loop-n-lock structure of proteins, providing the foundation for stability and designability of protein folds/domain and underlying their co-translational folding. Simplified protein sequences are considered here with the aim to explore the basic principles that presumably dominated the folding and stability of proteins in the early stages of structural evolution. Elementary functional loops (EFLs), closed loops with one or few catalytic residues, are, in turn, units of the protein function. They are apparent descendants of the prebiotic ring-like peptides, which gave rise to the first functional folds/domains being fused in the beginning of the evolution of protein structure. It is also shown how evolutionary relations between protein functional superfamilies and folds delineated with the help of EFLs can contribute to establishing the rules for design of desired enzymatic functions. Generalized descriptors of the elementary functions are proposed to be used as basic units in the future computational design.

Journal ArticleDOI
TL;DR: It is illustrated that monomer topology determines key aspects of domain-swapping and how symmetrized SBMs could be used to design domain- Swapping in proteins is explored.
Abstract: In domain-swapping, two or more identical protein monomers exchange structural elements and fold into dimers or multimers whose units are structurally similar to the original monomer. Domain-swapping is of biotechnological interest because inhibiting domain-swapping can reduce disease-causing fibrillar protein aggregation. To achieve such inhibition, it is important to understand both the energetics that stabilize the domain-swapped structure and the protein dynamics that enable the swapping. Structure-based models (SBMs) encode the folded structure of the protein in their potential energy functions. SBMs have been successfully used to understand diverse aspects of monomer folding. Symmetrized SBMs model interactions between two identical protein chains using only intra-monomer interactions. Molecular dynamics simulations of such symmetrized SBMs have been used to correctly predict the domain-swapped structure and to understand the mechanism of domain-swapping. Here, we review such models and illustrate that monomer topology determines key aspects of domain-swapping. However, in some proteins, specifics of local energetic interactions modulate domain-swapping and these need to be added to the symmetrized SBMs. We then summarize some general principles of the mechanism of domain-swapping that emerge from the symmetrized SBM simulations. Finally, using our own results, we explore how symmetrized SBMs could be used to design domain-swapping in proteins.

Journal ArticleDOI
TL;DR: Assessment of expression and remodeling of mechanosensitive K2P channels in atrial fibrillation (AF) and heart failure (HF) patients in comparison to murine models suggested a mechanistic contribution to cardiac arrhythmogenesis.
Abstract: Two-pore-domain potassium (K 2P ) channels modulate cellular excitability The significance of stretch-activated cardiac K 2P channels (K 2P 21, TREK-1, KCNK 2; K 2P 41, TRAAK, KCNK 4; K 2P 101, TREK-2, KCNK 10) in heart disease has not been elucidated in detail The aim of this work was to assess expression and remodeling of mechanosensitive K 2P channels in atrial fibrillation (AF) and heart failure (HF) patients in comparison to murine models Cardiac K 2P channel levels were quantified in atrial (A) and ventricular (V) tissue obtained from patients undergoing open heart surgery In addition, control mice and mouse models of AF (cAMP-response element modulator (CREM)-IbΔC-X transgenic animals) or HF (cardiac dysfunction induced by transverse aortic constriction, TAC) were employed Human and murine KCNK 2 displayed highest mRNA abundance among mechanosensitive members of the K 2P channel family (V > A) Disease-associated K 2P 21 remodeling was studied in detail In patients with impaired left ventricular function, atrial KCNK 2 (K 2P 21) mRNA and protein expression was significantly reduced In AF subjects, downregulation of atrial and ventricular KCNK 2 (K 2P 21) mRNA and protein levels was observed AF-associated suppression of atrial Kcnk 2 (K 2P 21) mRNA and protein was recapitulated in CREM-transgenic mice Ventricular Kcnk 2 expression was not significantly altered in mouse models of disease In conclusion, mechanosensitive K 2P 21 and K 2P 101 K + channels are expressed throughout the heart HF- and AF-associated downregulation of KCNK 2 (K 2P 21) mRNA and protein levels suggest a mechanistic contribution to cardiac arrhythmogenesis

Journal ArticleDOI
TL;DR: Modulatory effects of MEF that may contribute to increase the vulnerability to arrhythmia are discussed and MEF interaction with clinical conditions where mechanically induced changes in cardiac electrophysiology are likely to be more relevant are described.
Abstract: Mechano-electric feedback (MEF) is an established mechanism whereby myocardial deformation causes changes in cardiac electrophysiological parameters Extensive animal, laboratory and theoretical investigation has demonstrated that abnormal patterns of cardiac strain can induce alteration of electrical excitation and recovery through MEF, which can potentially contribute to the establishment of dangerous arrhythmias However, the clinical relevance of MEF in patients with heart disease remains to be established This paper reviews up-to date experimental evidence describing the response to different types of mechanical stimuli in the intact human heart with the support of new data collected during cardiac surgery It discusses modulatory effects of MEF that may contribute to increase the vulnerability to arrhythmia and describes MEF interaction with clinical conditions where mechanically induced changes in cardiac electrophysiology are likely to be more relevant Finally, directions for future studies, including the need for in-vivo human data providing simultaneous assessment of the distribution of structural, functional and electrophysiological parameters at the regional level, are identified

Journal ArticleDOI
TL;DR: Prospects for solving the folding-reaction paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models, which should explicitly include long-range force fields and local cell biological conditions.
Abstract: The current protein folding literature is reviewed. Two main approaches to the problem of folding were selected for this review: geometrical and biophysical. The geometrical approach allows the formulation of topological restrictions on folding, that are usually not taken into account in the construction of physical models. In particular, the topological constraints do not allow the known funnel-like energy landscape modeling, although most common methods of resolving the paradox are based on this method. The very paradox is based on the fact that complex molecules must reach their native conformations (complexes that result from reactions) in an exponentially long time, which clearly contradicts the observed experimental data. In this respect we considered the complexity of the reactions between ligands and proteins. On this general basis, the folding-reaction paradox was reformulated and generalized. We conclude that prospects for solving the paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models. However, such models should explicitly include long-range force fields and local cell biological conditions, such as structured water complexes and photon/phonon/soliton waves, ordered in discrete frequency bands. In this framework, collective and coherent oscillations in, and between, macromolecules are instrumental in inducing intra- and intercellular resonance, serving as an integral guiding network of life communication: the electrome aspect of the cell. Yet, to identify the actual mechanisms underlying the bonds between molecules (atoms), it will be necessary to perform dedicated experiments to more definitely solve the particular time paradox.

Journal ArticleDOI
TL;DR: It is suggested that both LIP US and LLLT may be beneficial to fracture healing in patients, and that LIPUS is more effective.
Abstract: The aim of this paper is to study the in vivo potency of low-level laser therapy (LLLT) and low intensity pulsed ultrasound (LIPUS) alone, accompanied by bone grafts, or accompanied by other factors on fracture healing in animal models and patients. In this paper, we aim to systematically review the published scientific literature regarding the use of LLLT and LIPUS to accelerate fracture healing in animal models and patients. We searched the PubMed database for the terms LLLT or LIPUS and/or bone, and fracture. Our analysis also suggests that both LIPUS and LLLT may be beneficial to fracture healing in patients, and that LIPUS is more effective. These finding are of considerable importance in those treatments with a LIPUS, as a laser device may reduce healing time. The most clinically relevant impact of the LIPUS treatment could be a significant reduction in the proportion of patients who go on to develop a nonunion. If it is confirmed that the therapeutic influence is true and reliable, patients will obtain benefits from LIPUS and LLLT. Further clinical trials of high methodological quality are needed in order to determine the optimal role of LIPUS and LLLT in fracture healing in patients.

Journal ArticleDOI
TL;DR: These model results suggest that known mechanisms of mechano-electric coupling in cardiac myocyte may be sufficient to be pro-arrhythmic, but only in combination and under specific strain patterns.
Abstract: Mechanically-induced alterations in cardiac electrophysiology are referred to as mechano-electric feedback (MEF), and play an important role in electrical regulation of cardiac performance. The influence of mechanical stress and strain on electrophysiology has been investigated at all levels, however the role of MEF in arrhythmia remains poorly understood. During the normal contraction of the heart, mechano-sensitive processes are an implicit component of cardiac activity. Under abnormal mechanical events, stretch-activated mechanisms may contribute to local or global changes in electrophysiology (EP). While such mechanisms have been hypothesised to be involved in mechanically-initiated arrhythmias, the details of these mechanisms and their importance remain elusive. We assess the theoretical role of stretch mechanisms using coupled models of cellular electrophysiology and sarcomere contraction dynamics. Using models of single ventricular myocytes, we first investigated the potential MEF contributions of stretch-activated currents (SAC), and stretch-induced myofilament calcium release, to test how strain and fibrosis may alter cellular electrophysiology. For all models investigated, SACs were alone not sufficient to create a pro-arrhythmic perturbation of the action potential with stretch. However, when combined with stretch-induced myofilament calcium release, the action potential could be shortened depending on the timing of the strain. This effect was highly model dependent, with a canine epicardial EP model being the most sensitive. These model results suggest that known mechanisms of mechano-electric coupling in cardiac myocyte may be sufficient to be pro-arrhythmic, but only in combination and under specific strain patterns.

Journal ArticleDOI
TL;DR: A genome-wide comparison of their transcriptomes by using an RNA-seq approach will explain the molecular mechanism of flavonoid synthesis in balck tartary buckwheat, but also provide the basis for further genomics research on this species or its allies.
Abstract: Black tartary buckwheat is recognized as 'black pearl' because of containg more rutin and other flavonoids as compared to yellow tartary buckwheat (traditional tartary buckwheat). Here, we show a genome-wide comparison of their transcriptomes by using an RNA-seq approach to elucidate the different molecular metabolism on the flowers from Black tartary buckwheat (HEIFENG No1) and yellow tartary buckwheat (XIQIAO No2). Over 48.4 million paired-end reads were assembled into 57,800 unigenes, of which about 57.9% (33, 472 unigenes) were annotated by BLAST searches in the NCBI non-redundant protein database. RPKM analysis showed that compared to YTB, the unigenes encoding phenylalanine ammonialyase (PAL), chalcone synthase (CHS) and chalcone isomerase (CHI) for early flavonoid synthesis and the unigene encoding quercetin 3-O-glucosyltransferase (UF3GT) for synthetizing rutin were at a higher level, but the unigene encoding Flavonol synthase (FLS) charging for kaempferol and quercetin synthesis at a lower level in BTB, which may be the reason for the higher content of rutin and the lower content of quercetin, the result obtained by HPLC, as confirmed by qRT-PCR analysis of these genes. The result will not only explain the molecular mechanism of flavonoid synthesis in balck tartary buckwheat, but also provide the basis for further genomics research on this species or its allies.

Journal ArticleDOI
TL;DR: This paper provides theoretical justifications for some common practices in the field for which a formal justification was missing and reviews the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.
Abstract: Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the “correct” threshold. In this paper we review the different concepts, their theoretical foundations and the derivation of their statistical distributions (the basis for establishing sensible thresholds). We provide theoretical justifications for some common practices in the field for which a formal justification was missing. We also analyze the relationship between SSNR and B-factors, the electron dose needed for achieving a given contrast and resolution, the number of images required, etc. Finally, we review the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.

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TL;DR: The history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data are focused on.
Abstract: Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies.

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TL;DR: The functional properties of the two-pore domain potassium (K2P) channel TREK-1, a major candidate for the cardiac SAK, are analyzed and the molecular mechanism of stretch-activation in K2P potassium channels is discussed.
Abstract: This review focuses on the role and the molecular candidates of the cardiac stretch-activated potassium current (SAK). The functional properties of the two-pore domain potassium (K2P) channel TREK-1, a major candidate for the cardiac SAK, are analyzed and the molecular mechanism of stretch-activation in K2P potassium channels is discussed. Furthermore, the functional modulation of TREK-1 by different cardiac interaction partners, as well as evidence for the functional role of the stretch-dependent TREK-1 and its putative subunits in the heart is reviewed. In addition, we summarize the recent evidence that TREK-1 is involved in the pathogenesis of human cardiac arrhythmias.

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TL;DR: This review demonstrates the potential of regulating lipid modifications that are essential for cell survival and discusses the concepts regarding their role in disease and therapeutics.
Abstract: The covalent attachment of lipids to proteins is a fundamental property of all living cells. These lipidated or lipid-modified proteins are directly targeted to the membranes and display diverse functional roles that are critical to cell function such as membrane signaling and trafficking. All lipidated proteins have been classified by the type of chemical moieties that are attached to them mainly palmitoylation, myristoylation, prenylation, cholesterylation, and addition of the Glycosylphosphatidyl inositol (GPI) anchor. Although the distinct hydrophobic lipid moiety largely dictates the functional compartmentalization, it also facilitates membrane trafficking and triggers a wide range of signaling pathways in cellular growth. In this review, we will focus on mechanistic insights underlying their membrane attachment, with a view to understand the regions that contribute to protein-membrane interface specificity. We also present a computational case study to report how different membrane lipids modulate insertion of the lipidated LC3 protein. Finally, in this review, we demonstrate the potential of regulating lipid modifications that are essential for cell survival and we discuss the concepts regarding their role in disease and therapeutics.

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TL;DR: Both, LLLT and LIPUS, apply a biostimulatory effect on osteoblasts, osteocytes, and enhance osteoblast proliferation and differentiation on different bony cell lines used in in vitro studies, and therefore, these may be useful tools for bone regeneration therapy.
Abstract: To compare the in vitro effectiveness of Low-Level Laser Therapy (LLLT) and Low Intensity Pulsed Ultrasound (LIPUS) on bony cells and related stem cells. In this study, we aim to systematically review the published scientific literature which explores the use of LLLT and LIPUS to biostimulate the activity or the proliferation of bony cells or stem cells in vitro. We searched the database PubMed for LLLT or LIPUS, with/without bone, osteoblast, osteocyte, stem cells, the human osteosarcoma cell line (MG63), bone-forming cells, and cell culture (or in vitro). These studies were subdivided into categories exploring the effect of LLLT or LIPUS on bony cells, stem cells, and other related cells. 75 articles were found between 1987 and 2016; these included: 50 full paper articles on LLLT and 25 full papers on LIPUS. These articles met the eligibility criteria and were included in our review. A detailed and concise description of the LLLT and the LIPUS protocols and their individual effects on bony cells or stem cells and their results are presented in five tables. Based on the main results and the conclusions of the reviewed articles in the current work, both, LLLT and LIPUS, apply a biostimulatory effect on osteoblasts, osteocytes, and enhance osteoblast proliferation and differentiation on different bony cell lines used in in vitro studies, and therefore, these may be useful tools for bone regeneration therapy. Moreover, in consideration of future cell therapy protocols, both, LLLT and LIPUS (especially LLLT), enhnce a significant increase in the initial number of SCs before differentiation, thus increasing the number of differentiated cells for tissue engineering, regenerative medicine, and healing. Further studies are necessary to determine the LLLT or the LIPUS parameters, which are optimal for biostimsulating bony cells and SCs for bone healing and regenerative medicine.

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TL;DR: This paper reviews and illustrates the diversity from several different aspects, involving the S-layer-carrying strains, the structure of S-layers, theS-layer proteins and genes, as well as the functions of S -layers.
Abstract: Surface layers, referred simply as S-layers, are the two-dimensional crystalline arrays of protein or glycoprotein subunits on cell surface. They are one of the most common outermost envelope components observed in prokaryotic organisms (Archaea and Bacteria). Over the past decades, S-layers have become an issue of increasing interest due to their ubiquitousness, special features and functions. Substantial work in this field provides evidences of an enormous diversity in S-layers. This paper reviews and illustrates the diversity from several different aspects, involving the S-layer-carrying strains, the structure of S-layers, the S-layer proteins and genes, as well as the functions of S-layers.