scholarly journals Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes

2021 ◽  
Vol 8 ◽  
Author(s):  
Péter Ecsédi ◽  
Gergő Gógl ◽  
László Nyitray
Keyword(s):  
Neurodegenerative Diseases ◽  
Structural Biology ◽  
Binding Proteins ◽  
Structural Information ◽  
Protein Complexes ◽  
Point Of View ◽  
S100 Proteins ◽  
Current State ◽  
Diverse World

S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.

scholarly journals The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1

2020 ◽  
Author(s):  
Sabrina Dietz ◽  
Miguel Vasconcelos Almeida ◽  
Emily Nischwitz ◽  
Jan Schreier ◽  
Nikenza Viceconte ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Wild Type ◽  
C Elegans ◽  
Double Stranded Dna ◽  
Telomere Sequence ◽  
Proteomics Approach

AbstractTelomeres are bound by dedicated protein complexes, like shelterin in mammals, which protect telomeres from DNA damage. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to screen for proteins binding to C. elegans telomeres, and identified TEBP-1 and TEBP-2, two paralogs that associate to telomeres in vitro and in vivo. TEBP-1 and TEBP-2 are expressed in the germline and during embryogenesis. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a mortal germline, a phenotype characterized by transgenerational germline deterioration. Notably, tebp-1; tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. TEBP-1 and TEBP-2 form a telomeric complex with the known single-stranded telomere-binding proteins POT-1, POT-2, and MRT-1. Furthermore, we find that POT-1 bridges the double- stranded binders TEBP-1 and TEBP-2, with the single-stranded binders POT-2 and MRT-1. These results describe the first telomere-binding complex in C. elegans, with TEBP-1 and TEBP-2, two double-stranded telomere binders required for fertility and that mediate opposite telomere dynamics.

scholarly journals The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity

2018 ◽  
Vol 1 (5) ◽  
pp. e201800187 ◽  
Author(s):  
Daniela Lazzaretti ◽  
Lina Bandholz-Cajamarca ◽  
Christiane Emmerich ◽  
Kristina Schaaf ◽  
Claire Basquin ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Structural Information ◽  
Target Selection ◽  
Mrna Localization ◽  
In Vitro Binding ◽  
Vitro Binding

During mRNA localization, RNA-binding proteins interact with specific structured mRNA localization motifs. Although several such motifs have been identified, we have limited structural information on how these interact with RNA-binding proteins. Staufen proteins bind structured mRNA motifs through dsRNA-binding domains (dsRBD) and are involved in mRNA localization in Drosophila and mammals. We solved the structure of two dsRBDs of human Staufen1 in complex with a physiological dsRNA sequence. We identified interactions between the dsRBDs and the RNA sugar–phosphate backbone and direct contacts of conserved Staufen residues to RNA bases. Mutating residues mediating nonspecific backbone interactions only affected Staufen function in Drosophila when in vitro binding was severely reduced. Conversely, residues involved in base-directed interactions were required in vivo even when they minimally affected in vitro binding. Our work revealed that Staufen can read sequence features in the minor groove of dsRNA and suggests that these influence target selection in vivo.

PMA induces stabilization of oncostatin M mRNA in human lymphoma U937 cells

2008 ◽  
Vol 410 (1) ◽  
pp. 177-186 ◽  
Author(s):  
Sumita Bandyopadhyay ◽  
Tapas K. Sengupta ◽  
Eleanor K. Spicer
Keyword(s):  
Binding Proteins ◽  
Protein Complexes ◽  
Oncostatin M ◽  
Dependent Manner ◽  
U937 Cells ◽  
Globin Mrna ◽  
Mrna Stabilization ◽  
Il Interleukin ◽  
Cell Extracts

OSM (oncostatin M) is a pleiotropic cytokine belonging to the IL (interleukin) 6 family that modulates the growth of some cancer cell lines. We have found that PMA treatment of human U937 lymphoma cells increased the steady-state levels of OSM mRNA. Furthermore, the half-life of OSM mRNA was increased from 2.3 to 6.2 h. Measurement of mRNA/hnRNA (heterogeneous nuclear RNA) ratios in PMA-treated cells suggests further that the increase in OSM mRNA is due to enhanced mRNA stability. Consistent with this, synthetic OSM mRNA transcripts decayed faster in extracts of untreated U937 cells than in extracts of PMA-treated cells. The 3′-untranslated region of OSM mRNA contains a putative ARE (AU-rich element) that may play a role in mRNA stabilization. Addition of the OSM ARE motif to the 3′-end of β-globin mRNA increased its decay rate in vitro. Decay assays with β-globin–AREOSM and β-globin transcripts indicate that PMA induces mRNA stabilization in an ARE-dependent manner. PMA also induces at least five OSM ARE-binding proteins. Supershift assays indicated that HuR is present in PMA-induced OSM mRNA–protein complexes. PMA treatment appears to induce translocation of HuR from the nucleus to the cytoplasm. RNA-decay assays indicated that HuR stabilizes OSM RNA in vitro. Additionally, immunodepletion of HuR from U937 cell extracts led to more rapid decay of OSM transcripts. Collectively, these findings suggest that the ARE plays a role in PMA-induced stabilization of OSM mRNA and that this process involves multiple ARE-binding proteins, including HuR.

scholarly journals Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

2021 ◽  
Author(s):  
Yuri Iozzo ◽  
Yu Qiu ◽  
Albert Xu ◽  
Anna Park ◽  
Maria Wendt ◽  
...  
Keyword(s):  
Decision Making ◽  
Structural Biology ◽  
Structural Information ◽  
Protein Complexes ◽  
Rapid Development ◽  
Protein Structures ◽  
Cost Effective ◽  
Particle Orientation ◽  
Dynamics Simulation ◽  
Rational Engineering

Developing a biologic medicine requires successful decision making at each step of selection, optimization, and/or combination of the right candidates at early research stages. Knowing the structural information and binding pattern between drug target and discovery candidates greatly increases the possibility of success. With the cryo-EM resolution revolution and rapid development of computational software, we have evaluated and integrated different tools in structural biology and the computation field and established a highly cost-effective platform, which allows us to obtain fast and accurate structural information for biologics projects with a close to 100% success rate and as fast as weeks turn-around time. Here we report four case studies selected from over 40 different protein structures and share how we integrate cryo-EM structure determination, computational structure modeling, and molecular dynamics simulation. With proper decision making and strategic planning, the platform allows us to obtain quality results within days to weeks, including sub-100 kDa complexes which are usually considered as a challenge due to their small size. Our utilization of this differential approach and use of multiple software packages, allows to manage priorities and resources to achieve goals quickly and efficiently. We demonstrate how to effectively overcome particle orientation bias by altering complex composition. In several of our examples, we use glycan density to facilitate interpretation of low-resolution 3D reconstruction and epitope mapping. Protein information plays an important role in our cryo-EM projects, especially in cases where we see significant challenges in obtaining high-resolution 3D maps.

scholarly journals Efficient and Specific Targeting of Polycomb Group Proteins Requires Cooperative Interaction between Grainyhead and Pleiohomeotic

2006 ◽  
Vol 26 (4) ◽  
pp. 1434-1444 ◽  
Author(s):  
András Blastyák ◽  
Rakesh K. Mishra ◽  
Francois Karch ◽  
Henrik Gyurkovics
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Cooperative Interaction ◽  
Protein Protein Interaction ◽  
Specific Targeting

ABSTRACT Specific targeting of the protein complexes formed by the Polycomb group of proteins is critically required to maintain the inactive state of a group of developmentally regulated genes. Although the role of DNA binding proteins in this process has been well established, it is still not understood how these proteins target the Polycomb complexes specifically to their response elements. Here we show that the grainyhead gene, which encodes a DNA binding protein, interacts with one such Polycomb response element of the bithorax complex. Grainyhead binds to this element in vitro. Moreover, grainyhead interacts genetically with pleiohomeotic in a transgene-based, pairing-dependent silencing assay. Grainyhead also interacts with Pleiohomeotic in vitro, which facilitates the binding of both proteins to their respective target DNAs. Such interactions between two DNA binding proteins could provide the basis for the cooperative assembly of a nucleoprotein complex formed in vitro. Based on these results and the available data, we propose that the role of DNA binding proteins in Polycomb group-dependent silencing could be described by a model very similar to that of an enhanceosome, wherein the unique arrangement of protein-protein interaction modules exposed by the cooperatively interacting DNA binding proteins provides targeting specificity.

scholarly journals Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information

2021 ◽  
Vol 9 ◽  
Author(s):  
Nicole Balasco ◽  
Carlo Diaferia ◽  
Giancarlo Morelli ◽  
Luigi Vitagliano ◽  
Antonella Accardo
Keyword(s):  
Neurodegenerative Diseases ◽  
Structural Biology ◽  
Structural Characterization ◽  
Structural Information ◽  
Data Bank ◽  
Spectroscopic Properties ◽  
Structural Motif ◽  
Peptide Chemistry ◽  
Research Areas

The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.

scholarly journals The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryoEM

IUCrJ ◽  
2019 ◽  
Vol 6 (2) ◽  
pp. 167-177 ◽  
Author(s):  
Stephen P. Muench ◽  
Svetlana V. Antonyuk ◽  
S. Samar Hasnain
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Structural Biology ◽  
Free Electron ◽  
Structural Information ◽  
Protein Complexes ◽  
Short Review ◽  
X Rays ◽  
Free Electron Lasers ◽  
X Ray

Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. The combination of results from X-ray free-electron lasers (XFELs), modern synchrotron crystallographic beamlines and cryo-electron microscopy (cryoEM) is proving to be particularly powerful. The highly brilliant undulator beamlines at modern synchrotron facilities have empowered the crystallographic revolution of high-throughput structure determination at high resolution. The brilliance of the X-rays at these crystallographic beamlines has enabled this to be achieved using microcrystals, but at the expense of an increased absorbed X-ray dose and a consequent vulnerability to radiation-induced changes. The advent of serial femtosecond crystallography (SFX) with X-ray free-electron lasers provides a new opportunity in which damage-free structures can be obtained from much smaller crystals (2 µm) and more complex macromolecules, including membrane proteins and multi-protein complexes. For redox enzymes, SFX provides a unique opportunity by providing damage-free structures at both cryogenic and ambient temperatures. The promise of being able to visualize macromolecular structures and complexes at high resolution without the need for crystals using X-rays has remained a dream, but recent technological advancements in cryoEM have made this come true and hardly a month goes by when the structure of a new/novel macromolecular assembly is not revealed. The uniqueness of cryoEM in providing structural information for multi-protein complexes, particularly membrane proteins, has been demonstrated by examples such as respirasomes. The synergistic use of cryoEM and crystallography in lead-compound optimization is highlighted by the example of the visualization of antimalarial compounds in cytochromebc1. In this short review, using some recent examples including our own work, we share the excitement of these powerful structural biology methods.

The role of mycotoxins in neurodegenerative diseases: current state of the art and future perspectives of research

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Vu Thu Thuy Nguyen ◽  
Svenja König ◽  
Simone Eggert ◽  
Kristina Endres ◽  
Stefan Kins
Keyword(s):  
Neurodegenerative Diseases ◽  
Research Field ◽  
Model Systems ◽  
Fungal Metabolites ◽  
Future Perspectives ◽  
Adverse Health Effects ◽  
Current State

Abstract Mycotoxins are fungal metabolites that can cause various diseases in humans and animals. The adverse health effects of mycotoxins such as liver failure, immune deficiency, and cancer are well-described. However, growing evidence suggests an additional link between these fungal metabolites and neurodegenerative diseases. Despite the wealth of these initial reports, reliable conclusions are still constrained by limited access to human patients and availability of suitable cell or animal model systems. This review summarizes knowledge on mycotoxins associated with neurodegenerative diseases and the assumed underlying pathophysiological mechanisms. The limitations of the common in vivo and in vitro experiments to identify the role of mycotoxins in neurotoxicity and thereby in neurodegenerative diseases are elucidated and possible future perspectives to further evolve this research field are presented.

scholarly journals Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners

2020 ◽  
Vol 21 (16) ◽  
pp. 5879
Author(s):  
Judith Weisz ◽  
Vladimir N. Uversky
Keyword(s):  
Calcium Binding ◽  
Binding Proteins ◽  
Intrinsically Disordered Proteins ◽  
Structural Information ◽  
S100 Proteins ◽  
Disordered Proteins ◽  
Dark Side ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
Ef Hand

Annexins and S100 proteins form two large families of Ca2+-binding proteins. They are quite different both structurally and functionally, with S100 proteins being small (10–12 kDa) acidic regulatory proteins from the EF-hand superfamily of Ca2+-binding proteins, and with annexins being at least three-fold larger (329 ± 12 versus 98 ± 7 residues) and using non-EF-hand-based mechanism for calcium binding. Members of both families have multiple biological roles, being able to bind to a large cohort of partners and possessing a multitude of functions. Furthermore, annexins and S100 proteins can interact with each other in either a Ca2+-dependent or Ca2+-independent manner, forming functional annexin-S100 complexes. Such functional polymorphism and binding indiscrimination are rather unexpected, since structural information is available for many annexins and S100 proteins, which therefore are considered as ordered proteins that should follow the classical “one protein–one structure–one function” model. On the other hand, the ability to be engaged in a wide range of interactions with multiple, often unrelated, binding partners and possess multiple functions represent characteristic features of intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs); i.e., functional proteins or protein regions lacking unique tertiary structures. The aim of this paper is to provide an overview of the functional roles of human annexins and S100 proteins, and to use the protein intrinsic disorder perspective to explain their exceptional multifunctionality and binding promiscuity.

scholarly journals The structure, functions and degradation of pigment-binding proteins of photosystem II.

2006 ◽  
Vol 53 (4) ◽  
pp. 693-708 ◽  
Author(s):  
Robert Luciński ◽  
Grzegorz Jackowski
Keyword(s):  
Photosystem Ii ◽  
Photosynthetic Pigments ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Structure Functions ◽  
Main Function ◽  
Core Complex ◽  
Current State ◽  
Pigment Protein Complexes ◽  
Psii Core Complex

Eleven proteins belonging to photosystem II (PSII) bind photosynthetic pigments in the form of thylakoid membrane-associated pigment-protein complexes. Five of them (PsbA, PsbB, PsbC, PsbD and PsbS) are assigned to PSII core complex while the remaining six (Lhcb1, Lhcb2, Lhcb3, Lhcb4, Lhcb5 and Lhcb6) constitute, along with their pigments, functional complexes situated more distantly with regard to P680 - the photochemical center of PSII. The main function of the pigment-binding proteins is to harvest solar energy and deliver it, in the form of excitation energy, ultimately to P680 although individual pigment-proteins may be engaged in other photosynthesis-related processes as well. The aim of this review is to present the current state of knowledge regarding the structure, functions and degradation of this family of proteins.

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