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Autophagy is a fundamental process in eukaryotic cells, essential for maintaining cellular homeostasis and promoting survival. This process involves the formation of a structure known as the autophagosome, which sequesters damaged cellular components such as misfolded proteins and dysfunctional organelles. These components are subsequently transported to lysosomes for degradation. Autophagy allows cells to withstand various stress conditions, including nutrient deprivation, hypoxia, and microbial infections. There are three primary types of autophagy: macroautophagy, microautophagy, and chaperone-mediated autophagy, each characterized by distinct mechanisms and features. The autophagy process is tightly regulated by autophagy-related genes (ATG) and consists of several stages: induction, autophagosome formation, fusion with lysosomes, and cargo degradation. Dysfunctional autophagy has been implicated in the development of various diseases, including cancer, neurodegenerative disorders, metabolic diseases, and bacterial or viral infections. Recent studies have highlighted the dual role of autophagy in cancer: while it can act as a tumor suppressor in early stages, it may also support tumor cell survival in advanced stages. In the nervous system, autophagy helps prevent the accumulation of harmful proteins and supports neuronal function. Additionally, autophagy plays a significant role in combating invasive pathogens, serving as a defensive mechanism against bacteria and viruses. Research indicates that autophagy is a promising target for developing new therapeutic strategies for a wide range of diseases. In-depth investigations into the molecular pathways regulating autophagy, particularly the mTOR and AMPK pathways, offer potential avenues for innovative treatments. This review provides a comprehensive analysis of the mechanisms and functions of autophagy, exploring its association with various human diseases. It presents a novel perspective on the potential clinical applications of autophagy, highlighting its role in the development of therapeutic strategies and deepening our understanding of this essential cellular process. [ABSTRACT FROM AUTHOR]

Clostridium botulinum strain Hall produces potent botulinum neurotoxin type A1, which causes food-borne, infant, and wound botulism in humans. Antibiotics and botulinum antitoxins can control growth and prevent botulinum toxicity. However, limited information on a protein with an unknown function hinders the discovery of new drug targets for this disease. In this study, a combined bioinformatics approach with literature support was applied to predict, assign, and validate operome functions. Our functional annotation scheme was based on sequence motifs, conserved domains, structures, protein folds, and evolutionary relationships. Approximately 14.62 % of the operome exhibited sequence similarity to known proteins, with 6.65 % predicted functions for 293 proteins, including 121 proteins exclusive to C. botulinum. Structural analysis revealed a significant presence of the Rossmann fold (26 %) and miscellaneous folds (43 %) among the operome. Transporters (>85) and transcriptional regulators (>45) were prevalent, underscoring their importance in C. botulinum adaptive strategies. The newly identified operome contributed to the diverse cellular and metabolic processes of this organism. The function of its operome was involved in amino acid metabolism and botulinum neurotoxin biosynthesis. In this study, we identified and characterized 13 new virulence proteins from the operome to determine their structure–function relationships. These new metabolic and virulence proteins allow the organism to colonize and interact with the human gastrointestinal tract. This study provides a quest for new drugs and targets for treating the underlying diseases of C. botulinum in humans.

Gliomas are the most common type of brain cancer, and among them, glioblastoma multiforme (GBM) is the most prevalent (about 60% of cases) and the most aggressive type of primary brain tumor. The treatment of GBM is a major challenge due to the pathophysiological characteristics of the disease, such as the presence of the blood-brain barrier (BBB), which prevents and regulates the passage of substances from the bloodstream to the brain parenchyma, making many of the chemotherapeutics currently available not able to reach the brain in therapeutic concentrations, accumulating in non-target organs, and causing considerable adverse effects for the patient. In this scenario, nanocarriers emerge as tools capable of improving the brain bioavailability of chemotherapeutics, in addition to improving their biodistribution and enhancing their uptake in GBM cells. This is possible due to its nanometric size and surface modification strategies, which can actively target nanocarriers to elements overexpressed by GBM cells (such as transmembrane receptors) related to aggressive development, drug resistance, and poor prognosis. In this review, an overview of the most frequently overexpressed receptors in GBM cells and possible approaches to chemotherapeutic delivery and active targeting using nanocarriers will be presented.

Nanocars are carbon‐based single‐molecules with a precise design that facilitates their atomic‐scale control on a surface. The rational design of these molecules is important in atomic and molecular‐scale manipulation to advance the development of molecular machines, as well as for a better understanding of self‐assembly, diffusion and desorption processes. Here, we introduce the molecular design and construction of a collection of minimalistic nanocars. They feature an anthracene chassis and four benzene derivatives as wheels. After sublimation and adsorption on an Au(111) surface, we show controlled and fast manipulation of the nanocars along the surface using the tip of a scanning tunneling microscope (STM). The mechanism behind the successful displacement is the induced dipole created over the nanocar by the STM tip. We utilized carbon monoxide functionalized tips both to avoid decomposition and accidentally picking the nanocars up during the manipulation. This strategy allowed thousands of maneuvers to successfully win the Nanocar Race II championship. [ABSTRACT FROM AUTHOR]

Plant cells contain two types of vacuoles, the lytic vacuole (LV) and protein storage vacuole (PSV). LVs are present in vegetative cells, whereas PSVs are found in seed cells. The physiological functions of the two types of vacuole differ. Newly synthesized proteins must be transported to these vacuoles via protein trafficking through the endomembrane system for them to function. Recently, significant advances have been made in elucidating the molecular mechanisms of protein trafficking to these organelles. Despite these advances, the relationship between the trafficking mechanisms to the LV and PSV remains unclear. Some aspects of the trafficking mechanisms are common to both types of vacuole, but certain aspects are specific to trafficking to either the LV or PSV. In this review, we summarize recent findings on the components involved in protein trafficking to both the LV and PSV and compare them to examine the extent of overlap in the trafficking mechanisms. In addition, we discuss the interconnection between the LV and PSV provided by the protein trafficking machinery and the implications for the identity of these organelles. [ABSTRACT FROM AUTHOR]

Methanobrevibacter ruminantium M1 (MRU) is a rod-shaped rumen methanogen with the ability to use H2 and CO2, and formate as substrates for methane formation in the ruminants. Enteric methane emitted from this organism can also be influential to the loss of dietary energy in ruminants and humans. To date, there is no successful technology to reduce methane due to a lack of knowledge on its molecular machinery and 73% conserved hypothetical proteins (HPs; operome) whose functions are still not ascertained perceptively. To address this issue, we have predicted and assigned a precise function to HPs and categorize them as metabolic enzymes, binding proteins, and transport proteins using a combined bioinformatics approach. The results of our study show that 257 (34%) HPs have well-defined functions and contributed essential roles in its growth physiology and host adaptation. The genome-neighborhood analysis identified 6 operon-like clusters such as hsp, TRAM, dsr, cbs and cas, which are responsible for protein folding, sudden heat-shock, host defense, and protection against the toxicities in the rumen. The functions predicted from MRU operome comprised of 96 metabolic enzymes with 17 metabolic subsystems, 31 transcriptional regulators, 23 transport, and 11 binding proteins. Functional annotation of its operome is thus more imperative to unravel the molecular and cellular machinery at the systems-level. The functional assignment of its operome would advance strategies to develop new anti-methanogenic targets to mitigate methane production. Hence, our approach provides new insight into the understanding of its growth physiology and lifestyle in the ruminants and also to reduce anthropogenic greenhouse gas emissions worldwide.

Methanobrevibacter ruminantium M1 (MRU) is a rod-shaped rumen methanogen with the ability to use H2 and CO2, and formate as substrates for methane formation in the ruminants. Enteric methane emitted from this organism can also be influential to the loss of dietary energy in ruminants and humans. To date, there is no successful technology to reduce methane due to a lack of knowledge on its molecular machinery and 73% conserved hypothetical proteins (HPs; operome) whose functions are still not ascertained perceptively. To address this issue, we have predicted and assigned a precise function to HPs and categorize them as metabolic enzymes, binding proteins, and transport proteins using a combined bioinformatics approach. The results of our study show that 257 (34%) HPs have well-defined functions and contributed essential roles in its growth physiology and host adaptation. The genome-neighborhood analysis identified 6 operon-like clusters such as hsp , TRAM, dsr , cbs and cas , which are responsible for protein folding, sudden heat-shock, host defense, and protection against the toxicities in the rumen. The functions predicted from MRU operome comprised of 96 metabolic enzymes with 17 metabolic subsystems, 31 transcriptional regulators, 23 transport, and 11 binding proteins. Functional annotation of its operome is thus more imperative to unravel the molecular and cellular machinery at the systems-level. The functional assignment of its operome would advance strategies to develop new anti-methanogenic targets to mitigate methane production. Hence, our approach provides new insight into the understanding of its growth physiology and lifestyle in the ruminants and also to reduce anthropogenic greenhouse gas emissions worldwide. [ABSTRACT FROM AUTHOR]

Coronary heart disease (CHD) is a common heart disease and the leading cause of cardiovascular death. Apoptosis and autophagy are two forms of programmed cell deaths which participate in the pathogenesis, development and prognosis of CHD. They are activated by several different pathways respectively and can interact with each other through the Beclin 1-Bcl-2/Bcl-xL complex, mTOR, TRAIL, TNF-α, ER stress and nucleus p53 pathways. Excessive apoptosis can promote myocardial ischemia, ischemia/reperfusion (I/R) injury, post-ischemia cardiac remodeling and coronary atherosclerosis except for VSMC-induced atherosclerosis progress. In contrast, activated autophagy protects heart from myocardial ischemia injury and post-ischemia cardiac remodeling, but can exert controversial effects on I/R injury and coronary atherosclerosis. Therefore, considering the pathological significance and mechanisms of apoptosis and autophagy underlying CHD, therapeutic implication of targeting apoptosis and autophagy is obvious. Fortunately, some therapeutic drugs and pharmacologic compounds involving mTOR inhibitor and AMPK activator have been reported to regulate apoptosis and autophagy. Although recent studies are limited and insufficient, they have pointed out the complex interplay between apoptosis and autophagy and further provided treatment concept for CHD by balancing the switch between the two responses. • Apoptosis and autophagy have complex interplays via different pathways. • Apoptosis promotes the pathogenesis of CHD generally. • Autophagy resists against myocardial ischemia and postischemia cardiac remodeling. • Autophagy plays controversial roles in I/R injury and coronary atherosclerosis. • Regulation of apoptosis and autophagy is an appealing therapy for CHD. [ABSTRACT FROM AUTHOR]

Vacuoles are one of the most prominent organelles in plant cells, and they play various important roles, such as degradation of waste materials, storage of ions and metabolites, and maintaining turgor. During the past two decades, numerous advances have been made in understanding how proteins are specifically delivered to the vacuole. One of the most crucial steps in this process is specific sorting of soluble vacuolar proteins. Vacuolar sorting receptors (VSRs), which are type I membrane proteins, are involved in the sorting and packaging of soluble vacuolar proteins into transport vesicles with the help of various accessory proteins. To date, large amounts of data have led to the development of two different models describing VSR-mediated vacuolar trafficking that are radically different in multiple ways, particularly regarding the location of cargo binding to, and release from, the VSR and the types of carriers utilized. In this review, we summarize current literature aimed at elucidating VSR-mediated vacuolar trafficking and compare the two models with respect to the sorting signals of vacuolar proteins, as well as the molecular machinery involved in VSR-mediated vacuolar trafficking and its action mechanisms.

A mini-review: As the top-down approach for miniaturisation of technology reaches its inherent limitations, robust strategies to build nanoscale machinery components, which have the ability to convert an input energy into motion, from the molecular level up, become increasingly important. Nature is certainly the most proficient in the control of molecular level motion; nevertheless, many successes have been enjoyed in the pursuit of mimicking key aspects of nature’s molecular machines, including two state switches, ion pumps, unidirectional rotary motors and molecular robots that can move molecular cargo. This mini-review outlines of some of the most impressive recent examples towards this end. [ABSTRACT FROM AUTHOR]

Over the last few decades, concepts of protein intrinsic disorder have been implicated in different biological processes. Recent studies have suggested that intrinsically disordered proteins (IDPs) provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion in host cells. In case of Zika virus, the roles of protein intrinsic disorder in mechanisms of pathogenesis are not completely understood. In this study, we have analyzed the prevalence of intrinsic disorder in Zika virus proteome (strain MR 766). Our analyses revealed that Zika virus polyprotein is enriched with intrinsically disordered protein regions (IDPRs) and this finding is consistent with previous reports on the involvement of IDPs in shell formation and virulence of the Flaviviridae family. We found abundant IDPRs in Capsid, NS2B, NS3, NS4A, and NS5 proteins that are involved in mature particle formation and replication. In our view, the intrinsic disorder-focused analysis of ZIKV proteins could be important for the development of new disorder-based drugs.

Over the last few decades, concepts of protein intrinsic disorder have been implicated in different biological processes. Recent studies have suggested that intrinsically disordered proteins (IDPs) provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion in host cells. In case of Zika virus, the roles of protein intrinsic disorder in mechanisms of pathogenesis are not completely understood. In this study, we have analyzed the prevalence of intrinsic disorder in Zika virus proteome (strain MR 766). Our analyses revealed that Zika virus polyprotein is enriched with intrinsically disordered protein regions (IDPRs) and this finding is consistent with previous reports on the involvement of IDPs in shell formation and virulence of the Flaviviridae family. We found abundant IDPRs in Capsid, NS2B, NS3, NS4A, and NS5 proteins that are involved in mature particle formation and replication. In our view, the intrinsic disorder-focused analysis of ZIKV proteins could be important for the development of disorder-based drugs. [ABSTRACT FROM AUTHOR]

All living organisms have acquired the outstanding ability to overcome the limitations imposed by changeable environments through the gain of genetic traits over years of evolution and the tendency of individuals to associate in communities. The complementation of a singular weakness, the deployment of reinforcement for the good of the community, the better use of resources, or effective defense against external aggression are advantages gained by this communal behavior. Communication has been the cohesive element prompting the global responses that promote efficiency in two features of any community: specialization in differentiated labor and the spatio-temporal organization of the environment. These principles illustrate that what we call human ecology also applies to the cellular world and is exemplified in eukaryotic organisms, where sophisticated cell-to-cell communication networks coordinate cell differentiation and the specialization of multiple tissues consisting of numerous cells embedded in a multifunctional extracellular matrix. This sophisticated molecular machinery appears, however, to be invented by the "simple" but still fascinating bacteria. What I will try to expand in the following sections are notions of how "single prokaryotic cells" organize a multicellular community. [ABSTRACT FROM AUTHOR]

Molecular Machinery, Nanocars, Scanning Tunneling Microscopy, [4+2] Cycloaddition This nanomachine was able to win the Nanocar Race II championship, as reported by Jonas Björk, Emilio M. Pérez, David Écija et al. in their Research Article (e202212395). Keywords: Molecular Machinery; Nanocars; Scanning Tunneling Microscopy; [4+2] Cycloaddition EN Molecular Machinery Nanocars Scanning Tunneling Microscopy [4+2] Cycloaddition 1 1 1 01/31/23 20230201 NES 230201 B A minimalistic hydrocarbon nanocar b was synthesized, deposited on a Au(111) surface, and driven by a STM tip thanks to electrostatic interactions. [Extracted from the article]

Molecular Machinery, Nanocars, Scanning Tunneling Microscopy, [4+2] Cycloaddition Inside Cover: Design and Manipulation of a Minimalistic Hydrocarbon Nanocar on Au(111) (Angew. Keywords: Molecular Machinery; Nanocars; Scanning Tunneling Microscopy; [4+2] Cycloaddition EN Molecular Machinery Nanocars Scanning Tunneling Microscopy [4+2] Cycloaddition 1 1 1 01/31/23 20230201 NES 230201 B A minimalistic hydrocarbon nanocar b was synthesized, deposited on a Au(111) surface, and driven by a STM tip thanks to electrostatic interactions. [Extracted from the article]

A pivotal guest role: A new porphyrin polymer, poly(PorZn⋅DD) (see picture, pink/purple), composed of a porphyrinatozinc and a porphyrin double‐decker complex as a repeating unit was synthesized. In poly(PorZn⋅DD), porphyrinatozinc complexes recognize a divalent amine (tan/red) to induce an intramolecular pivoting motion through the rotation of porphyrin double‐decker complexes and the polymer undergoes shortening and compaction. [ABSTRACT FROM AUTHOR]

Abstract: A macrocyclic host molecule that comprised two different rotating modules, cerium(IV) bis(porphyrinate)s and ferrocenyl rotating units, exhibiting contraction/expansion motion was synthesized, which can be regarded as a prototype of artificial molecular spring driven by cooperative guest binding in 1:6 stoichiometry. [Copyright &y& Elsevier]

A model of muscle contraction is proposed, assuming loose coupling between power strokes and ATP hydrolysis of a myosin head. The energy borrowing mechanism is introduced in a cross-bridge cycle that borrows energy from the environment to cover the necessary energy for enthalpy production during sliding movement. Important premises for modeling are as follows: 1) the interaction area where a myosin head slides is supposed to be on an actin molecule; 2) the actomyosin complex is assumed to generate force F(θ) , which slides the myosin head M* in the interaction area; 3) the direction of the force F(θ) varies in proportion to the load P; 4) the energy supplied by ATP hydrolysis is used to retain the myosin head in the high-energy state M*, and is not used for enthalpy production; 5) the myosin head enters a hydration state and dehydration state repeatedly during the cross-bridge cycle. The dehydrated myosin head recovers its hydrated state by hydration in the surrounding medium; 6) the energy source for work and heat production liberated by the AM* complex is of external origin. On the basis of these premises, the model adequately explains the experimental results observed at various levels in muscular samples: 1) twist in actin filaments observed in shortening muscle fibers; 2) the load-velocity relationship in single muscle fiber; 3) energy balance among enthalpy production, the borrowed energy and the energy supplied by ATP hydrolysis during muscle contraction. Force F(θ?) acting on the myosin head is depicted. [ABSTRACT FROM AUTHOR]

Intracellular organelles are membrane-bound and biochemically distinct compartments constructed to serve specialized functions in eukaryotic cells. Through extensive interactions, they form networks to coordinate and integrate their specialized functions for cell physiology. A fundamental property of these organelle networks is that they constantly undergo dynamic organization via membrane fusion and fission to remodel their internal connections and to mediate direct material exchange between compartments. The dynamic organization not only enables them to serve critical physiological functions adaptively but also differentiates them from many other biological networks such as gene regulatory networks and cell signaling networks. This review examines this fundamental property of the organelle networks from a systems point of view. The focus is exclusively on homotypic networks formed by mitochondria, lysosomes, endosomes, and the endoplasmic reticulum, respectively. First, key mechanisms that drive the dynamic organization of these networks are summarized. Then, several distinct organizational properties of these networks are highlighted. Next, spatial properties of the dynamic organization of these networks are emphasized, and their functional implications are examined. Finally, some representative molecular machineries that mediate the dynamic organization of these networks are surveyed. Overall, the dynamic organization of intracellular organelle networks is emerging as a fundamental and unifying paradigm in the internal organization of eukaryotic cells. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology., (© 2020 Wiley Periodicals LLC.)