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10 pages, 1705 KiB

Open AccessArticle

Quantitative Visualization of the Interaction between Complement Component C1 and Immunoglobulin G: The Effect of C_H1 Domain Deletion

by Saeko Yanaka, Shigetaka Nishiguchi, Rina Yogo, Hiroki Watanabe, Jiana Shen, Hirokazu Yagi, Takayuki Uchihashi and Koichi Kato

Int. J. Mol. Sci. 2022, 23(4), 2090; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23042090 - 14 Feb 2022

Cited by 1 | Viewed by 2298

Abstract

Immunoglobulin G (IgG) adopts a modular multidomain structure that mediates antigen recognition and effector functions, such as complement-dependent cytotoxicity. IgG molecules are self-assembled into a hexameric ring on antigen-containing membranes, recruiting the complement component C1q. In order to provide deeper insights into the [...] Read more.

Immunoglobulin G (IgG) adopts a modular multidomain structure that mediates antigen recognition and effector functions, such as complement-dependent cytotoxicity. IgG molecules are self-assembled into a hexameric ring on antigen-containing membranes, recruiting the complement component C1q. In order to provide deeper insights into the initial step of the complement pathway, we report a high-speed atomic force microscopy study for the quantitative visualization of the interaction between mouse IgG and the C1 complex composed of C1q, C1r, and C1s. The results showed that the C1q in the C1 complex is restricted regarding internal motion, and that it has a stronger binding affinity for on-membrane IgG2b assemblages than C1q alone, presumably because of the lower conformational entropy loss upon binding. Furthermore, we visualized a 1:1 stoichiometric interaction between C1/C1q and an IgG2a variant that lacks the entire C_H1 domain in the absence of an antigen. In addition to the canonical C1q-binding site on Fc, their interactions are mediated through a secondary site on the C_L domain that is cryptic in the presence of the C_H1 domain. Our findings offer clues for novel-modality therapeutic antibodies. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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25 pages, 5471 KiB

Open AccessArticle

The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT

by Julie Ledoux, Alain Trouvé and Luba Tchertanov

Int. J. Mol. Sci. 2022, 23(3), 1589; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031589 - 29 Jan 2022

Cited by 4 | Viewed by 1757

Abstract

RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling [...] Read more.

RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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15 pages, 3415 KiB

Open AccessArticle

Oligomeric Structural Transition of HspB1 from Chinese Hamster

by Nina Kurokawa, Rio Midorikawa, Manami Nakamura, Keiichi Noguchi, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama and Masafumi Yohda

Int. J. Mol. Sci. 2021, 22(19), 10797; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910797 - 06 Oct 2021

Cited by 1 | Viewed by 1501

Abstract

HspB1 is a mammalian sHsp that is ubiquitously expressed in almost all tissues and involved in regulating many vital functions. Although the recent crystal structure of human HspB1 showed that 24 monomers form the oligomeric complex of human HspB1 in a spherical configuration, [...] Read more.

HspB1 is a mammalian sHsp that is ubiquitously expressed in almost all tissues and involved in regulating many vital functions. Although the recent crystal structure of human HspB1 showed that 24 monomers form the oligomeric complex of human HspB1 in a spherical configuration, the molecular architecture of HspB1 is still controversial. In this study, we examined the oligomeric structural change of CgHspB1 by sedimentation velocity analytical ultracentrifugation. At the low temperature of 4 °C, CgHspB1 exists as an 18-mer, probably a trimeric complex of hexamers. It is relatively unstable and partially dissociates into small oligomers, hexamers, and dodecamers. At elevated temperatures, the 24-mer was more stable than the 18-mer. The 24-mer is also in dynamic equilibrium with the dissociated oligomers in the hexameric unit. The hexamer further dissociates to dimers. The disulfide bond between conserved cysteine residues seems to be partly responsible for the stabilization of hexamers. The N-terminal domain is involved in the assembly of dimers and the interaction between hexamers. It is plausible that CgHspB1 expresses a chaperone function in the 24-mer structure. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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15 pages, 3736 KiB

Open AccessArticle

Molecular Biomechanics Controls Protein Mixing and Segregation in Adherent Membranes

by Long Li, Bernd Henning Stumpf and Ana-Sunčana Smith

Int. J. Mol. Sci. 2021, 22(7), 3699; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22073699 - 02 Apr 2021

Cited by 4 | Viewed by 2499

Abstract

Cells interact with their environment by forming complex structures involving a multitude of proteins within assemblies in the plasma membrane. Despite the omnipresence of these assemblies, a number of questions about the correlations between the organisation of domains and the biomechanical properties of [...] Read more.

Cells interact with their environment by forming complex structures involving a multitude of proteins within assemblies in the plasma membrane. Despite the omnipresence of these assemblies, a number of questions about the correlations between the organisation of domains and the biomechanical properties of the involved proteins, namely their length, flexibility and affinity, as well as about the coupling to the elastic, fluctuating membrane, remain open. Here we address these issues by developing an effective Kinetic Monte Carlo simulation to model membrane adhesion. We apply this model to a typical experiment in which a cell binds to a functionalized solid supported bilayer and use two ligand-receptor pairs to study these couplings. We find that differences in affinity and length of proteins forming adhesive contacts result in several characteristic features in the calculated phase diagrams. One such feature is mixed states occurring even with proteins with length differences of 10 nm. Another feature are stable nanodomains with segregated proteins appearing on time scales of cell experiments, and for biologically relevant parameters. Furthermore, we show that macroscopic ring-like patterns can spontaneously form as a consequence of emergent protein fluxes. The capacity to form domains is captured by an order parameter that is founded on the virial coefficients for the membrane mediated interactions between bonds, which allow us to collapse all the data. These findings show that taking into account the role of the membrane allows us to recover a number of experimentally observed patterns. This is an important perspective in the context of explicit biological systems, which can now be studied in significant detail. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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Review

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13 pages, 27083 KiB

Open AccessReview

Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding

by Soichiro Kawagoe, Koichiro Ishimori and Tomohide Saio

Int. J. Mol. Sci. 2022, 23(5), 2485; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23052485 - 24 Feb 2022

Cited by 1 | Viewed by 4392

Abstract

Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires [...] Read more.

Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics–activity relationships to explain the mechanism of functional diversity of molecular chaperones. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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21 pages, 3076 KiB

Open AccessReview

Current Understanding of Molecular Phase Separation in Chromosomes

by Je-Kyung Ryu, Da-Eun Hwang and Jeong-Mo Choi

Int. J. Mol. Sci. 2021, 22(19), 10736; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910736 - 04 Oct 2021

Cited by 13 | Viewed by 4413

Abstract

Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and [...] Read more.

Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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20 pages, 2779 KiB

Open AccessReview

Structural Characterization of Receptor–Receptor Interactions in the Allosteric Modulation of G Protein-Coupled Receptor (GPCR) Dimers

by Raudah Lazim, Donghyuk Suh, Jai Woo Lee, Thi Ngoc Lan Vu, Sanghee Yoon and Sun Choi

Int. J. Mol. Sci. 2021, 22(6), 3241; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22063241 - 22 Mar 2021

Cited by 5 | Viewed by 7051

Abstract

G protein-coupled receptor (GPCR) oligomerization, while contentious, continues to attract the attention of researchers. Numerous experimental investigations have validated the presence of GPCR dimers, and the relevance of dimerization in the effectuation of physiological functions intensifies the attractiveness of this concept as a [...] Read more.

G protein-coupled receptor (GPCR) oligomerization, while contentious, continues to attract the attention of researchers. Numerous experimental investigations have validated the presence of GPCR dimers, and the relevance of dimerization in the effectuation of physiological functions intensifies the attractiveness of this concept as a potential therapeutic target. GPCRs, as a single entity, have been the main source of scrutiny for drug design objectives for multiple diseases such as cancer, inflammation, cardiac, and respiratory diseases. The existence of dimers broadens the research scope of GPCR functions, revealing new signaling pathways that can be targeted for disease pathogenesis that have not previously been reported when GPCRs were only viewed in their monomeric form. This review will highlight several aspects of GPCR dimerization, which include a summary of the structural elucidation of the allosteric modulation of class C GPCR activation offered through recent solutions to the three-dimensional, full-length structures of metabotropic glutamate receptor and γ-aminobutyric acid B receptor as well as the role of dimerization in the modification of GPCR function and allostery. With the growing influence of computational methods in the study of GPCRs, we will also be reviewing recent computational tools that have been utilized to map protein–protein interactions (PPI). Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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19 pages, 1856 KiB

Open AccessReview

Pneumoviral Phosphoprotein, a Multidomain Adaptor-Like Protein of Apparent Low Structural Complexity and High Conformational Versatility

by Christophe Cardone, Claire-Marie Caseau, Nelson Pereira and Christina Sizun

Int. J. Mol. Sci. 2021, 22(4), 1537; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041537 - 03 Feb 2021

Cited by 10 | Viewed by 1992

Abstract

Mononegavirales phosphoproteins (P) are essential co-factors of the viral polymerase by serving as a linchpin between the catalytic subunit and the ribonucleoprotein template. They have highly diverged, but their overall architecture is conserved. They are multidomain proteins, which all possess an oligomerization domain [...] Read more.

Mononegavirales phosphoproteins (P) are essential co-factors of the viral polymerase by serving as a linchpin between the catalytic subunit and the ribonucleoprotein template. They have highly diverged, but their overall architecture is conserved. They are multidomain proteins, which all possess an oligomerization domain that separates N- and C-terminal domains. Large intrinsically disordered regions constitute their hallmark. Here, we exemplify their structural features and interaction potential, based on the Pneumoviridae P proteins. These P proteins are rather small, and their oligomerization domain is the only part with a defined 3D structure, owing to a quaternary arrangement. All other parts are either flexible or form short-lived secondary structure elements that transiently associate with the rest of the protein. Pneumoviridae P proteins interact with several viral and cellular proteins that are essential for viral transcription and replication. The combination of intrinsic disorder and tetrameric organization enables them to structurally adapt to different partners and to act as adaptor-like platforms to bring the latter close in space. Transient structures are stabilized in complex with protein partners. This class of proteins gives an insight into the structural versatility of non-globular intrinsically disordered protein domains. Full article

(This article belongs to the Special Issue Biophysical Characterization and Molecular Engineering of Multidomain Proteins 2.0)

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