scholarly journals In vivo aspects of protein folding and quality control

Science ◽  
2016 ◽  
Vol 353 (6294) ◽  
pp. aac4354 ◽  
Author(s):  
David Balchin ◽  
Manajit Hayer-Hartl ◽  
F. Ulrich Hartl
Keyword(s):  
Molecular Chaperones ◽  
Three Dimensional ◽  
Pharmacological Intervention ◽  
Folding Pathway ◽  
Protein Homeostasis ◽  
Protein Chain ◽  
Biological Functions ◽  
Integrated Network ◽  
Cellular Environment

Most proteins must fold into unique three-dimensional structures to perform their biological functions. In the crowded cellular environment, newly synthesized proteins are at risk of misfolding and forming toxic aggregate species. To ensure efficient folding, different classes of molecular chaperones receive the nascent protein chain emerging from the ribosome and guide it along a productive folding pathway. Because proteins are structurally dynamic, constant surveillance of the proteome by an integrated network of chaperones and protein degradation machineries is required to maintain protein homeostasis (proteostasis). The capacity of this proteostasis network declines during aging, facilitating neurodegeneration and other chronic diseases associated with protein aggregation. Understanding the proteostasis network holds the promise of identifying targets for pharmacological intervention in these pathologies.

The general concept of molecular chaperones

1993 ◽  
Vol 339 (1289) ◽  
pp. 257-261 ◽  
Keyword(s):  
Heat Shock ◽  
Molecular Chaperones ◽  
Self Assembly ◽  
General Concept ◽  
Biological Functions ◽  
Protein Surfaces ◽  
Cellular Processes ◽  
Introductory Article ◽  
Protein Molecules

This introductory article proposes a conceptual framework in which to consider the information that is emerging about the proteins called molecular chaperones, and suggests some definitions that may be useful in this new field of biochemistry. Molecular chaperones are currently defined in functional terms as a class of unrelated families of protein that assist the correct non-covalent assembly of other polypeptide-containing structures in vivo , but which are not components of these assembled structures when they are performing their normal biological functions. The term assembly in this definition embraces not only the folding of newly synthesized polypeptides and any association into oligomers that may occur, but also includes any changes in the degree of either folding or association that may take place when proteins carry out their functions, are transported across membranes, or are repaired or destroyed after stresses such as heat shock. Known molecular chaperones do not convey steric information essential for correct assembly, but appear to act by binding to interactive protein surfaces that are transiently exposed during various cellular processes; this binding inhibits incorrect interactions that may otherwise produce non-functional structures. Thus the concept of molecular chaperones does not contradict the principle of protein self-assembly, but qualifies it by suggesting that in vivo self-assembly requires assistance by other protein molecules.

scholarly journals GroEL/ES buffers entropic traps in folding pathway during evolution of a model substrate

2020 ◽  
Author(s):  
Anwar Sadat ◽  
Satyam Tiwari ◽  
Kanika Verma ◽  
Arjun Ray ◽  
Mudassar Ali ◽  
...  
Keyword(s):  
Protein Folding ◽  
Molecular Chaperones ◽  
Folding Pathway ◽  
Substrate Protein ◽  
Model Protein ◽  
Physical Barriers ◽  
Evolutionary Step ◽  
Entropic Traps

ABSTRACTThe folding landscape of proteins can change during evolution with the accumulation of mutations that may introduce entropic or enthalpic barriers in the protein folding pathway, making it a possible substrate of molecular chaperones in vivo. Can the nature of such physical barriers of folding dictate the feasibility of chaperone-assistance? To address this, we have simulated the evolutionary step to chaperone-dependence keeping GroEL/ES as the target chaperone and GFP as a model protein in an unbiased screen. We find that the mutation conferring GroEL/ES dependence in vivo and in vitro encode an entropic trap in the folding pathway rescued by the chaperonin. Additionally, GroEL/ES can edit the formation of non-native contacts similar to DnaK/J/E machinery. However, this capability is not utilized by the substrates in vivo. As a consequence, GroEL/ES caters to buffer mutations that predominantly cause entropic traps, despite possessing the capacity to edit both enthalpic and entropic traps in the folding pathway of the substrate protein.

scholarly journals Unfolding the chaperone story

2017 ◽  
Vol 28 (22) ◽  
pp. 2919-2923 ◽  
Author(s):  
F. Ulrich Hartl
Keyword(s):  
Protein Folding ◽  
Molecular Chaperones ◽  
Current Concept ◽  
Cellular Process ◽  
Protein Chain ◽  
Native State ◽  
Folding Process ◽  
Spontaneous Process ◽  
Short Essay

Protein folding in the cell was originally assumed to be a spontaneous process, based on Anfinsen’s discovery that purified proteins can fold on their own after removal from denaturant. Consequently cell biologists showed little interest in the protein folding process. This changed only in the mid and late 1980s, when the chaperone story began to unfold. As a result, we now know that in vivo, protein folding requires assistance by a complex machinery of molecular chaperones. To ensure efficient folding, members of different chaperone classes receive the nascent protein chain emerging from the ribosome and guide it along an ordered pathway toward the native state. I was fortunate to contribute to these developments early on. In this short essay, I will describe some of the critical steps leading to the current concept of protein folding as a highly organized cellular process.

The T-Knot Motif Revisited

1999 ◽  
Vol 380 (10) ◽  
pp. 1247-1250 ◽  
Author(s):  
Fabio Polticelli ◽  
Stefano Pascarella ◽  
Domenico Bordo ◽  
Martino Bolognesi ◽  
Paolo Ascenzi
Keyword(s):  
Secondary Structure ◽  
Structural Feature ◽  
Three Dimensional ◽  
Structural Motif ◽  
Loop Length ◽  
Protein Chain ◽  
Hydrophobic Core ◽  
Biological Functions ◽  
Β Sheet

Abstract The T-knot scaffold, a disulphide-reinforced structural motif shared by several proteins with very different biological functions, has been defined as ‘a stretch of the protein chain which comprises two strands of a β-sheet and three loops, knotted by two disulphides into the shape of the letter T’. In this communication we show that the presence of a central β-sheet is not a required structural feature for proteins sharing the T-knot topology. Moreover, superposition of the three-dimensional structures of representative members of the T-knot family highlights a common and structurally well-defined core, formed by the two knotted disulphides, substituting for a larger residue-based hydrophobic core. These results suggest that folding and stability of the T-knot scaffold mainly depend on the geometry of the two knotted disulphides and on the loop length, and that the secondary structure elements are not a prerequisite for motif formation. Accordingly, a redefinition of the T-knot motif is proposed.

scholarly journals PITHD1 is a proteasome-interacting protein essential for male fertilization

2020 ◽  
Vol 295 (6) ◽  
pp. 1658-1672 ◽  
Author(s):  
Hiroyuki Kondo ◽  
Takafumi Matsumura ◽  
Mari Kaneko ◽  
Kenichi Inoue ◽  
Hidetaka Kosako ◽  
...  
Keyword(s):  
Cell Cycle Regulation ◽  
T Cell Development ◽  
Proteasome Activity ◽  
Protein Homeostasis ◽  
Biological Functions ◽  
Interacting Protein ◽  
Thymic Epithelium ◽  
Cycle Regulation ◽  
Deficient Mice

The proteasome is a protein-degrading molecular complex that is necessary for protein homeostasis and various biological functions, including cell cycle regulation, signal transduction, and immune response. Proteasome activity is finely regulated by a variety of proteasome-interacting molecules. PITHD1 is a recently described molecule that has a domain putatively capable of interacting with the proteasome. However, it is unknown whether PITHD1 can actually bind to proteasomes and what it does in vivo. Here we report that PITHD1 is detected specifically in the spermatids in the testis and the cortical thymic epithelium in the thymus. Interestingly, PITHD1 associates with immunoproteasomes in the testis, but not with thymoproteasomes in the thymus. Mice deficient in PITHD1 exhibit severe male infertility accompanied with morphological abnormalities and impaired motility of spermatozoa. Furthermore, PITHD1 deficiency reduces proteasome activity in the testis and alters the amount of proteins that are important for fertilization capability by the sperm. However, the PITHD1-deficient mice demonstrate no detectable defects in the thymus, including T cell development. Collectively, our results identify PITHD1 as a proteasome-interacting protein that plays a nonredundant role in the male reproductive system.

scholarly journals Protein Homeostasis Database: protein quality control in E.coli

2019 ◽  
Author(s):  
Reshmi Ramakrishnan ◽  
Bert Houben ◽  
Łukasz Kreft ◽  
Alexander Botzki ◽  
Joost Schymkowitz ◽  
...  
Keyword(s):  
Quality Control ◽  
Molecular Chaperones ◽  
Protein Quality ◽  
Trigger Factor ◽  
Proteolytic Degradation ◽  
Whole Genome ◽  
Protein Homeostasis ◽  
Web Interface ◽  
Nascent Chain

Abstract Motivation In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these. Results We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets. Availability and implementation The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.

scholarly journals Bridging the gap betweenin vitroandin vivoRNA folding

2016 ◽  
Vol 49 ◽  
Author(s):  
Kathleen A. Leamy ◽  
Sarah M. Assmann ◽  
David H. Mathews ◽  
Philip C. Bevilacqua
Keyword(s):  
Rna Structure ◽  
Rna Folding ◽  
Three Dimensional ◽  
Molecular Crowding ◽  
Cellular Processes ◽  
Cellular Environment ◽  
Folding Pathways ◽  
And Function

AbstractDeciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functionsin vivo. Within the last few years, methods have been developed to probe RNA structuresin vivoand genome-wide. These studies reveal that RNA often adopts very different structuresin vivoandin vitro, and provide profound insights into RNA biology. Nonetheless, bothin vitroandin vivoapproaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studiesin vitrooften lack direct cellular relevance, leaving a gap in our knowledge of RNA foldingin vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under suchin vivo-likeconditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA foldingin vitroandin vivoand discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell.

scholarly journals Photodynamic Therapy-Mediated Immune Responses in Three-Dimensional Tumor Models

2021 ◽  
Vol 22 (23) ◽  
pp. 12618
Author(s):  
Nkune Williams Nkune ◽  
Nokuphila Winifred Nompumelelo Simelane ◽  
Hanieh Montaseri ◽  
Heidi Abrahamse
Keyword(s):  
Photodynamic Therapy ◽  
Immune Responses ◽  
Three Dimensional ◽  
Tumor Model ◽  
Experimental Models ◽  
Cellular Heterogeneity ◽  
Tumor Models ◽  
Cellular Environment

Photodynamic therapy (PDT) is a promising non-invasive phototherapeutic approach for cancer therapy that can eliminate local tumor cells and produce systemic antitumor immune responses. In recent years, significant efforts have been made in developing strategies to further investigate the immune mechanisms triggered by PDT. The majority of in vitro experimental models still rely on the two-dimensional (2D) cell cultures that do not mimic a three-dimensional (3D) cellular environment in the human body, such as cellular heterogeneity, nutrient gradient, growth mechanisms, and the interaction between cells as well as the extracellular matrix (ECM) and therapeutic resistance to anticancer treatments. In addition, in vivo animal studies are highly expensive and time consuming, which may also show physiological discrepancies between animals and humans. In this sense, there is growing interest in the utilization of 3D tumor models, since they precisely mimic different features of solid tumors. This review summarizes the characteristics and techniques for 3D tumor model generation. Furthermore, we provide an overview of innate and adaptive immune responses induced by PDT in several in vitro and in vivo tumor models. Future perspectives are highlighted for further enhancing PDT immune responses as well as ideal experimental models for antitumor immune response studies.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

Three-Dimensional Subcellular Organization of Hepatocytes in Intact Liver: Simultaneous Visualization of Cytoskeletal and Membrane Markers by Confocal Microscopy

1996 ◽  
Vol 54 ◽  
pp. 288-289
Author(s):  
Greg V. Martin ◽  
Ann L. Hubbard
Keyword(s):  
Three Dimensional ◽  
Integral Membrane Proteins ◽  
Polarized Secretion ◽  
Microscope Images ◽  
Computer Aided ◽  
Intracellular Organelles ◽  
Cytoskeletal Elements ◽  
Simultaneous Visualization

The microtubule (MT) cytoskeleton is necessary for many of the polarized functions of hepatocytes. Among the functions dependent on the MT-based cytoskeleton are polarized secretion of proteins, delivery of endocytosed material to lysosomes, and transcytosis of integral plasma membrane (PM) proteins. Although microtubules have been shown to be crucial to the establishment and maintenance of functional and structural polarization in the hepatocyte, little is known about the architecture of the hepatocyte MT cytoskeleton in vivo, particularly with regard to its relationship to PM domains and membranous organelles. Using an in situ extraction technique that preserves both microtubules and cellular membranes, we have developed a protocol for immunofluorescent co-localization of cytoskeletal elements and integral membrane proteins within 20 µm cryosections of fixed rat liver. Computer-aided 3D reconstruction of multi-spectral confocal microscope images was used to visualize the spatial relationships among the MT cytoskeleton, PM domains and intracellular organelles.

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