Subcellular Systems Research Articles

Recent Advances in pH and Redox Responsive Polymer Nanocomposites for Cancer Therapy

Cancer therapy currently focuses on personalized targeted treatments. A promising approach uses stimuli-responsive biomaterials for site-specific drug release, such as pH- and redox-triggered polymer nanocomposites. These materials respond to the tumor microenvironment, enhance efficacy, and reduce off-target effects. Cancer cells with anomalous properties such as acidic cytosolic pH and elevated redox potential are targeted by these biomaterials. An imbalance in ions and biological thiols in the cytoplasm contributes to tumor growth. Functionalized polymer nanocomposites with large surface areas and specific targeting outperform conventional small-molecule materials. To overcome problems such as low bioavailability, uncontrolled drug release, and poor cell penetration, multifunctional nanomaterials make it easier for drugs to enter certain cellular or subcellular systems. High therapeutic efficacy is achieved through surface functionalization, site-specific targeting, and the use of stimuli-responsive components. In particular, pH and redox dual-stimuli-based polymeric nanocomposites for cancer therapeutics have scarcely been reported. This article provides recent progress in pH- and redox-responsive polymer nanocomposites for site-specific drug delivery in cancer therapy. It explores the design principles, fabrication methods, mechanisms of action, and prospects of these dual-stimuli-responsive biomaterials.

Unraveling Complexities in the Absorption and Disposition Kinetics of Abiraterone via Iterative PBPK Model Development and Refinement.

Abiraterone is a first-in-class inhibitor of cytochrome P450 17A1 (CYP17A1), and its pharmacokinetic (PK) profile is susceptible to intrinsic and extrinsic variabilities. Potential associations between abiraterone concentrations and pharmacodynamic consequences in prostate cancer may demand further dosage optimization to balance therapeutic outcomes. Consequently, we aim to develop a physiologically based pharmacokinetic (PBPK) model for abiraterone via a middle-out approach to prospectively interrogate the untested, albeit clinically relevant, scenarios. To characterize in vivo hydrolysis of prodrug abiraterone acetate (AA) and supersaturation of abiraterone, in vitro aqueous solubility data, biorelevant measurements, and supersaturation and precipitation parameters were utilized for mechanistic absorption simulation. CYP3A4-mediated N-oxidation and sulfotransferase 2A1-catalyzed sulfation of abiraterone were subsequently quantified in human liver subcellular systems. Iterative PBPK model refinement involved evaluation of potential organic anion transporting polypeptide (OATP)-mediated abiraterone uptake in transfected cells in the absence and presence of albumin. The developed PBPK model recapitulated the duodenal concentration-time profile of both AA and abiraterone after simulated AA administration. Our findings established abiraterone as a substrate of hepatic OATP1B3 to recapitulate its unbound metabolic intrinsic clearance. Further consideration of a transporter-induced protein-binding shift established accurate translational scaling factors and extrapolated the sinusoidal uptake process. Subsequent simulations effectively predicted the PK of abiraterone upon single and multiple dosing. Our systematic development of the abiraterone PBPK model has demonstrated its application for the prospective interrogation of the individual or combined influences of potential interindividual variabilities influencing the systemic exposure of abiraterone.

Dynamic cycling with a unique Hsp90/Hsp70-dependent chaperone machinery and GAPDH is needed for heme insertion and activation of neuronal NO synthase

Heat shock protein 90 (Hsp90) is known to mediate heme insertion and activation of heme-deficient neuronal nitric oxide (NO) synthase (apo-nNOS) in cells by a highly dynamic interaction that has been extremely difficult to study mechanistically with the use of subcellular systems. In that the heme content of many critical hemeproteins is regulated by Hsp90 and the heme chaperone GAPDH, the development of an invitro system for the study of this chaperone-mediated heme regulation would be extremely useful. Here, we show that use of an antibody-immobilized apo-nNOS led not only to successful assembly of chaperone complexes but the ability to show a clear dependence on Hsp90 and GAPDH for heme-mediated activation of apo-nNOS. The kinetics of binding for Hsp70 and Hsp90, the ATP and K+ dependence, and the absolute requirement for Hsp70 in assembly of Hsp90•apo-nNOS heterocomplexes all point to a similar chaperone machinery to the well-established canonical machine regulating steroid hormone receptors. However, unlike steroid receptors, the use of a purified protein system containing Hsp90, Hsp70, Hsp40, Hop, and p23 is unable to activate apo-nNOS. Thus, heme insertion requires a unique Hsp90-chaperone complex. With this newly developed invitro system, which recapitulates the cellular process requiring GAPDH as well as Hsp90, further mechanistic studies are now possible to better understand the components of the Hsp90-based chaperone system as well as how this heterocomplex works with GAPDH to regulate nNOS and possibly other hemeproteins.

Therapeutic Advancements in Metal and Metal Oxide Nanoparticle-Based Radiosensitization for Head and Neck Cancer Therapy.

Simple SummaryThough radiation therapy remains a primary modality for head and neck cancer (HNC) management, the collateral damage to normal surrounding tissues and tumor relapse represent major challenges. Hence, it is imperative to develop safer and more effective HNC therapies. Metal and metal oxide nanoparticle-based radiosensitizers have been explored for their potential to overcome these challenges. The key impetus of this review was to shed light on ongoing metal and metal oxide nanoparticle-based radiosensitizers’ development and to address their success in in vitro and in vivo HNC models and in clinical translation.Although radiation therapy (RT) is one of the mainstays of head and neck cancer (HNC) treatment, innovative approaches are needed to further improve treatment outcomes. A significant challenge has been to design delivery strategies that focus high doses of radiation on the tumor tissue while minimizing damage to surrounding structures. In the last decade, there has been increasing interest in harnessing high atomic number materials (Z-elements) as nanoparticle radiosensitizers that can also be specifically directed to the tumor bed. Metallic nanoparticles typically display chemical inertness in cellular and subcellular systems but serve as significant radioenhancers for synergistic tumor cell killing in the presence of ionizing radiation. In this review, we discuss the current research and therapeutic efficacy of metal nanoparticle (MNP)-based radiosensitizers, specifically in the treatment of HNC with an emphasis on gold- (AuNPs), gadolinium- (AGdIX), and silver- (Ag) based nanoparticles together with the metallic oxide-based hafnium (Hf), zinc (ZnO) and iron (SPION) nanoparticles. Both in vitro and in vivo systems for different ionizing radiations including photons and protons were reviewed. Finally, the current status of preclinical and clinical studies using MNP-enhanced radiation therapy is discussed.

Modern Ideas about the Mechanisms of Action of Ultraviolet Radiation on Cells and Subcellular Systems

Modern Ideas about the Mechanisms of Action of Ultraviolet Radiation on Cells and Subcellular Systems

A multi-scale map of cell structure fusing protein images and interactions.

The cell is a multi-scale structure with modular organization across at least four orders of magnitude1. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately2,3. Here we integrate immunofluorescence images in the Human Protein Atlas4 with affinity purifications in BioPlex5 to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.

In Vitro Liver Metabolism of Six Flavonoid C-Glycosides.

Several medical plants belonging to the genera Passiflora, Viola, and Crataegus accumulate flavonoid C-glycosides, which likely contribute to their efficacy. Information regarding their phase I and II metabolism in the liver are lacking. Thus, in vitro liver metabolism of orientin, isoorientin, schaftoside, isoschaftoside, vitexin, and isovitexin, all of which accumulated in Passiflora incarnata L., was investigated by incubation in subcellular systems with human liver microsomes and human liver S9 fraction. All metabolite profiles were comprehensively characterized using HPLC-DAD and UHPLC–MS/MS analysis. Mono-glycosylic flavones of the luteolin-type orientin and isoorientin showed a broad range of mono-glucuronidated and mono-sulfated metabolites, whereas for mono-glycosylic flavones of the apigenin-type vitexin and isovitexin, only mono-glucuronidates could be detected. For di-glycosylic flavones of the apigenin-type schaftosid and isoschaftosid, no phase I or II metabolites were identified. The main metabolite of isoorientin was isolated using solid-phase extraction and prep. HPLC-DAD and identified as isoorientin-3′-O-α-glucuronide by NMR analysis. A second isolated glucuronide was assigned as isoorientin 4′-O-α-glucuronide. These findings indicate that vitexin and isovitexin are metabolized preferentially by uridine 5′-diphospho glucuronosyltransferases (UGTs) in the liver. As only orientin and isoorientin showed mono-sulfated and mono-glucuronidated metabolites, the dihydroxy group in 3′,4′-position may be essential for additional sulfation by sulfotransferases (SULTs) in the liver. The diglycosylic flavones schaftoside and isoschaftoside are likely not accepted as substrates of the used liver enzymes under the chosen conditions.

Large-scale analysis reveals spatiotemporal circadian patterns of cilia transcriptomes in the primate brain.

Cilia are dynamic subcellular systems, with core structural and functional components operating in a highly coordinated manner. Since many environmental stimuli sensed by cilia are circadian in nature, it is reasonable to speculate that genes encoding cilia structural and functional components follow rhythmic circadian patterns of expression. Using computational methods and the largest spatiotemporal gene expression atlas of primates, we identified and analyzed the circadian rhythmic expression of cilia genes across 22 primate brain areas. We found that around 73% of cilia transcripts exhibited circadian rhythmicity across at least one of 22 brain regions. In 12 brain regions, cilia transcriptomes were significantly enriched with circadian oscillating transcripts, as compared to the rest of the transcriptome. The phase of the cilia circadian transcripts deviated from the phase of the majority of the background circadian transcripts, and transcripts coding for cilia basal body components accounted for the majority of cilia circadian transcripts. In addition, adjacent or functionally connected brain nuclei had large overlapping complements of circadian cilia genes. Most remarkably, cilia circadian transcripts shared across the basal ganglia nuclei and the prefrontal cortex peaked in these structures in sequential fashion that is similar to the sequential order of activation of the basal ganglia-cortical circuitry in connection with movement coordination, albeit on completely different timescales. These findings support a role for the circadian spatiotemporal orchestration of cilia gene expression in the normal physiology of the basal ganglia-cortical circuit and motor control. Studying orchestrated cilia rhythmicity in the basal ganglia-cortical circuits and other brain circuits may help develop better functional models, and shed light on the causal effects cilia functions have on these circuits and on the regulation of movement and other behaviors.

Mathematical Modeling in Biology: Part 2. Models of Protein Interaction Processes in a Photosynthetic Membrane

The second part of the article concerns agent-based, multiparticle, Brownian and molecular dynamic models. In these models, the motion and interaction of individual proteins—electron carriers (Brownian multiparticle models) and individual atoms in molecules—electron carriers and their complexes (molecular dynamics) are described based on the apparatus of Brownian and molecular modeling. Direct multiparticle models explicitly simulate the Brownian diffusion of mobile protein carriers and their electrostatic interactions with multienzyme complexes, both in solution and in the interior of a biomembrane. Analysis of these models reveals the role of diffusion and electrostatic factors in the regulation of electron transport, the effect of the of reaction volume geometry, and ionic strength and pH of the cell medium on the rate of electron transport reactions between protein carriers. Through joint application methods of kinetic and Brownian multiparticle modeling make it possible to study the regulation mechanisms of electron transport processes at the subcellular and molecular levels and also mechanisms of electron-flow switching in plant and algae cells and to evaluate the optimal conditions for the obtainment of target products in microalgae cells, e.g., hydrogen as an alternative fuel. The prospects for various methods of mathematical modeling used to study subcellular systems are discussed in the conclusion. The paper is based on the results obtained at the Department of Biophysics, Biological Faculty, Moscow State University.

Abstract IA-09: Mapping cell structure across scales by fusing protein images and interactions

Abstract Cancer cells are multi-scale structures with modular organization across at least four orders of magnitude. Two central approaches for mapping this structure – protein fluorescent imaging and protein interaction – each generate extensive datasets but of distinct qualities and resolutions that are typically treated separately. Here, I will describe ongoing efforts to reconcile the large-scale data emerging from protein imaging and protein affinity purification interaction screens to create unified maps of cancer cells. The core concept is to use machine learning to compute a suitable embedding for each dataset, then to use these data embeddings to produce a general measure of protein distance calibrated against cellular components of known size. The evolving map, called the Multi-Scale Integrated Cell (MuSIC 1.0), currently resolves 69 subcellular systems of which approximately half are undocumented. Based on these findings we have performed 134 additional affinity purifications, validating close subunit associations for the majority of systems. I will also discuss how these cell maps can be used to identify protein complexes, and larger-scale systems such as organelles, that are under significant selective pressure for somatic mutations in different tumor types. In many of these cases, the mutation burden of the complex is far more substantial than the mutation frequency of any of the individual genes that encode it. By integration across scales, MuSIC substantially increases the mapping resolution obtained from imaging while giving protein interactions a spatial dimension, paving the way to incorporate many molecular data types in proteome-wide maps of cells. This work is a collaboration between the Cancer Cell Mapping Initiative (CCMI), the Human Protein Atlas (HPA), and the BioPlex Resource. Citation Format: Trey Ideker. Mapping cell structure across scales by fusing protein images and interactions [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr IA-09.

The Unusual Suspects in Cytokinesis: Fitting the Pieces Together.

Cytokinesis is the step of the cell cycle in which the cell must faithfully separate the chromosomes and cytoplasm, yielding two daughter cells. The assembly and contraction of the contractile network is spatially and temporally coupled with the formation of the mitotic spindle to ensure the successful completion of cytokinesis. While decades of studies have elucidated the components of this machinery, the so-called usual suspects, and their functions, many lines of evidence are pointing to other unexpected proteins and sub-cellular systems as also being involved in cytokinesis. These we term the unusual suspects. In this review, we introduce recent discoveries on some of these new unusual suspects and begin to consider how these subcellular systems snap together to help complete the puzzle of cytokinesis.

Biomarkers to quantify cell migration characteristics

BackgroundBecause cell movement is primarily driven by the connection between F-actin and integrin through a physical linkage, cellular elasticity and adhesion strength have been considered as biomarkers of cell motility. However, a consistent set of biomarkers that indicate the potential for cell motility is still lacking.MethodsIn this work, we characterize a phenotype of cell migration in terms of cellular elasticity and adhesion strength, which reveals the interdependence of subcellular systems that mediate optimal cell migration.ResultsStiff cells weakly adhered to the substrate revealed superior motility, while soft cell migration with strong adhesion was relatively inhibited. The spatial distribution and amount of F-actin and integrin were highly variable depending on cell type, but their density exhibited linear correlations with cellular elasticity and adhesion strength, respectively.ConclusionsThe densities of F-actin and integrin exhibited linear correlations with cellular elasticity and adhesion strength, respectively, therefore, they can be considered as biomarkers to quantify cell migration characteristics.

Signaling Pathways in Immune Responses with Incomplete Information: A Novel Model Founded on Coupled Uniform Sequential Reaction Systems

A novel mathematical model for determining the forms of signaling pathways, ranging from linear structures to networks, on the basis of single-mode and multimodal time courses of immune responses under the condition of incomplete information, was elaborated. The subcellular immune processes and systems lacking the kinetic parameters still remain, in general, undetermined by deterministic quantitative models, which has resulted in the resignation from these models in favor of the so-called kinetically agnostic models. The model proposed in this paper intends to give a deterministic description of signaling pathways implicated in immune responses with unknown kinetic parameters. To do that, uniform sequential reaction systems and coupled sequential reaction systems were constructed using systems of differential equations and the novel notions of uniform functions, transition, coupling and branch operations founded on the assumptions of a uniform distribution of unknown rate constants, mass action kinetics, and first-order kinetics. Reaction step-dependent analytical solutions to the uniform sequential systems were expressed by the means of the incomplete gamma function and unambiguously characterized using, amongst others, the Lambert W function, which were necessary to obtain strict analytical solutions to those systems. These systems were validated by comparing their solutions with those obtained for ordinary sequential systems, regarded as the systems with complete information. The numerical solutions to the uniform sequential systems obtained by the Lederberg-Marquardt method were compared with those obtained by the Lambert W function. The signaling pathways were determined by analyzing the uniform sequential and coupled sequential reaction systems that describe the time courses of multimodal immune responses. Bi- and tri-modal immune processes representing temporal expressions of the transcription factor T-bet, the IL-12Rβ2 receptor, the IL-4, Tbx21 and Twist1 genes—all in helper T cells, calcium ion in 2G12.1 T cell hybridoma, c-Fos sumoylation in serum-stimulated HeLa cells, and IFN-γ-secreting cytotoxic T cells were modeled. Application of the coupled uniform sequential systems to the above immune processes allowed accurate approximations of their time behavior and to determine the structures of the signaling pathways and to predict some. A notion of the fractional reaction step, and its meaning in revealing the coupled sequential systems behind the seeming sequential ones, was introduced and analyzed. A consistent approach to the different forms of signaling pathways, beginning from the linear sequential systems through coupled (nonlinear) sequential ones to networks, was presented together with an algebraic insight into those systems.

Near-infrared templated fluorescent probe for nitroxyl: Selective and sensitive turn-on detection in living cells

Bioactive species, including reactive oxygen species, reactive nitrogen species, and reactive sulfur species, play important roles in physiological processes; thus, it is very valuable to monitor such species in subcellular systems. Herein, for the first time, we report a turn-on highly red-emissive near-infrared (NIR) fluorescent probe, LF3 (3), for nitroxyl (HNO) which is composed of a triphenylphosphine moiety and possesses long-wavelength emission (740−840 nm), to the best of our knowledge. The probe, LF3, is highly selective and sensitive for HNO with a response time of 6 min and a detection limit as low as 15 nM. The quantum yield values LF3 and HNO added LF3 obtained from the fluorescence studies are 0.005 and 0.264, respectively. More importantly, LF3 is able to image both exogenous and endogenous nitroxyl in living cells without any interference from the background fluorescence.

Functional Innovation in the Evolution of the Calcium-Dependent System of the Eukaryotic Endoplasmic Reticulum.

The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca2+)-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function including signal transduction, motility, division, and biomineralization. We use comparative genomics and sensitive sequence and structure analyses to investigate the evolution of this system. Our findings reconstruct the core form of the Ca2+-stores system in the last eukaryotic common ancestor as having at least 15 proteins that constituted a basic system for facilitating both Ca2+ flux across endomembranes and Ca2+-dependent signaling. We present evidence that the key EF-hand Ca2+-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgard archaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca2+-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca2+-stores system, even though no prokaryotic lineage possesses a comparable system. Further, using quantitative measures derived from comparative genomics we show that there were several rounds of lineage-specific gene expansions, innovations of novel gene families, and gene losses correlated with biological innovation such as the biomineralized molluscan shells, coccolithophores, and animal motility. The burst of innovation of new genes in animals included the wolframin protein associated with Wolfram syndrome in humans. We show for the first time that it contains previously unidentified Sel1, EF-hand, and OB-fold domains, which might have key roles in its biochemistry.

Models for Understanding Resistance to Chemotherapy in Liver Cancer.

The lack of response to pharmacological treatment constitutes a substantial limitation in the handling of patients with primary liver cancers (PLCs). The existence of active mechanisms of chemoresistance (MOCs) in hepatocellular carcinoma, cholangiocarcinoma, and hepatoblastoma hampers the usefulness of chemotherapy. A better understanding of MOCs is needed to develop strategies able to overcome drug refractoriness in PLCs. With this aim, several experimental models are commonly used. These include in vitro cell-free assays using subcellular systems; studies with primary cell cultures; cancer cell lines or heterologous expression systems; multicellular models, such as spheroids and organoids; and a variety of in vivo models in rodents, such as subcutaneous and orthotopic tumor xenografts or chemically or genetically induced liver carcinogenesis. Novel methods to perform programmed genomic edition and more efficient techniques to isolate circulating microvesicles offer new opportunities for establishing useful experimental tools for understanding the resistance to chemotherapy in PLCs. In the present review, using three criteria for information organization: (1) level of research; (2) type of MOC; and (3) type of PLC, we have summarized the advantages and limitations of the armamentarium available in the field of pharmacological investigation of PLC chemoresistance.

Cell Fuelling and Metabolic Energy Conservation in Synthetic Cells.

We are aiming for a blue print for synthesizing (moderately complex) subcellular systems from molecular components and ultimately for constructing life. However, without comprehensive instructions and design principles, we rely on simple reaction routes to operate the essential functions of life. The first forms of synthetic life will not make every building block for polymers de novo according to complex pathways, rather they will be fed with amino acids, fatty acids and nucleotides. Controlled energy supply is crucial for any synthetic cell, no matter how complex. Herein, we describe the simplest pathways for the efficient generation of ATP and electrochemical ion gradients. We have estimated the demand for ATP by polymer synthesis and maintenance processes in small cell-like systems, and we describe circuits to control the need for ATP. We also present fluorescence-based sensors for pH, ionic strength, excluded volume, ATP/ADP, and viscosity, which allow the major physicochemical conditions inside cells to be monitored and tuned.

Correlated random walks inside a cell: actin branching and microtubule dynamics.

Correlated random walks (CRW) have been explored in many settings, most notably in the motion of individuals in a swarm or flock. But some subcellular systems such as growth or disassembly of bio-polymers can also be described with similar models and understood using related mathematical methods. Here we consider two examples of growing cytoskeletal elements, actin and microtubules. We use CRW or generalized CRW-like PDEs to model their spatial distributions. In each case, the linear models can be reduced to a Telegrapher's equation. A combination of explicit solutions (in one case) and numerical solutions (in the other) demonstrates that the approach to steady state can be accompanied by (decaying) waves.

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

High Performance Computing with Coarse Grained Model of Biological Macromolecules

The Unified Coarse Grained Model of biological macromolecules (UCGM) that is being developed in our laboratory is a model designed to carry out large-scale simulations of biological macromolecules. The simplified chain representation used in the model allows to obtain 3-4 orders of magnitude extention of the time-scale of simulations, compared to that of all-atom simulations. Unlike most of the other coarse-grained force fields, UCGM is a physics-based force field, independent of structural databases and applicable to treat non-standard systems. In this communication, the efficiency and scalability of the new version of UCGM package with Fortran 90, with two parallelization levels: coarse-grained and fine-grained, is reported for systems with various size and oligomeric state. The performance was tested in the canonical- and replica exchange MD mode, with small- and moderate-size proteins and protein complexes (20 to 1,636 amino-acid residues), as well as with large systems such as, e.g., human proteosome 20S with size over 6,200 aminoacid residues, which show the advantage of using coarse-graining. It is demonstrated that, with using massively parallel architectures, and owing to the physics-based nature of UCGM, real-time simulations of the behavior of subcellular systems are feasible.