Inference of Structure and Dynamic Order of Formation of Multimeric Protein Complexes

2021 ◽  
pp. 93-112
Author(s):  
Carlos A. Del Carpio ◽  
Eiichiro Ichiishi
Keyword(s):  
Protein Complexes ◽  
Multimeric Protein

scholarly journals Inflammasomes inMycobacterium tuberculosis-Driven Immunity

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Sebastian Wawrocki ◽  
Magdalena Druszczynska
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Inflammatory Response ◽  
Immune Responses ◽  
Proinflammatory Cytokines ◽  
Immune Cells ◽  
Protein Complexes ◽  
Inflammasome Activation ◽  
Host Immune Responses ◽  
Multimeric Protein

The development of effective innate and subsequent adaptive host immune responses is highly dependent on the production of proinflammatory cytokines that increase the activity of immune cells. The key role in this process is played by inflammasomes, multimeric protein complexes serving as a platform for caspase-1, an enzyme responsible for proteolytic cleavage of IL-1βand IL-18 precursors. Inflammasome activation, which triggers the multifaceted activity of these two proinflammatory cytokines, is a prerequisite for developing an efficient inflammatory response against pathogenicMycobacterium tuberculosis(M.tb). This review focuses on the role of NLRP3 and AIM2 inflammasomes inM.tb-driven immunity.

Interaction with complement proteins and dendritic cells implicates LCCL domain-containing proteins (CCps) of malaria parasites in immunomodulation

2018 ◽  
Vol 475 (21) ◽  
pp. 3311-3314 ◽  
Author(s):  
Puran Singh Sijwali
Keyword(s):  
Dendritic Cells ◽  
Complement System ◽  
Protein Complexes ◽  
Immune Defense ◽  
Malaria Parasites ◽  
Classical Complement Pathway ◽  
Soluble Immune Complexes ◽  
Multimeric Protein ◽  
The Complement System

The evasion of host immune defense is critical for pathogens to invade, establish infection and perpetuate in the host. The complement system is one of the first lines of innate immune defense in humans that destroys pathogens in the blood circulation. Activation of the complement system through direct encounter with pathogens or some other agents leads to osmolysis of pathogens, clearance of soluble immune complexes and recruitment of lymphocytes at the site of activation. Although malaria parasites are not exposed to the complement system owing to their intracellular development for most part of their life cycle in the human host, the extracellular stages must face the complement system of human or mosquito or both. In a recent issue of the Biochemical Journal, Sharma et al. reported that Plasmodiumfalciparum LCCL domain-containing protein 1 (PfCCp1) inhibited activation of the classical complement pathway and down-regulated effector responses of dendritic cells, which implicate PfCCp1 and related proteins in immunomodulation of the host that likely benefits the parasite. PfCCp1 belongs to a multi-domain protein family that exists as multimeric protein complexes. It needs to be investigated whether PfCCp1 or its multimeric protein complexes have an immunomodulatory effect in vivo and on the mosquito complement system

scholarly journals Computational Prediction of Heteromeric Protein Complex Disassembly Order with Hybrid Monte Carlo/Molecular Dynamics Simulation

2022 ◽  
Author(s):  
Ikuo Kurisaki ◽  
Shigenori Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Complex ◽  
Protein Complexes ◽  
Structural Bioinformatics ◽  
Dynamics Simulation ◽  
Tryptophan Synthase ◽  
Selection Scheme ◽  
Hybrid Monte Carlo ◽  
Multimeric Protein

The physicochemical entity of biological phenomenon in the cell is a network of biochemical reactions and the activity of such a network is regulated by multimeric protein complexes. Mass spectroscopy (MS) experiments and multimeric protein docking simulations based on structural bioinformatics techniques have revealed the molecular-level stoichiometry and static configuration of subcomplexes in their bound forms, then revealing the subcomplex populations and formation orders. Meanwhile, these methodologies are not designed to straightforwardly examine temporal dynamics of multimeric protein assembly and disassembly, essential physicochemical properties to understand functional expression mechanisms of proteins in the biological environment. To address the problem, we had developed an atomistic simulation in the framework of the hybrid Monte Carlo/Molecular Dynamics (hMC/MD) method and succeeded in observing disassembly of homomeric pentamer of the serum amyloid P component protein in experimentally consistent order. In this study, we improved the hMC/MD method to examine disassembly processes of the tryptophan synthase tetramer, a paradigmatic heteromeric protein complex in MS studies. We employed the likelihood-based selection scheme to determine a dissociation-prone subunit pair at each hMC/MD simulation cycle and achieved highly reliable predictions of the disassembly orders with the success rate over 0.9 without a priori knowledge of the MS experiments and structural bioinformatics simulations. We similarly succeeded in reliable predictions for the other three tetrameric protein complexes. These achievements indicate the potential availability of our hMC/MD approach as the general purpose methodology to obtain microscopic and physicochemical insights into multimeric protein complex formation.

scholarly journals Crystallizing the 6S and 8S spliceosomal assembly intermediates: a complex project

2015 ◽  
Vol 71 (10) ◽  
pp. 2040-2053 ◽  
Author(s):  
Jann-Patrick Pelz ◽  
Hermann Schindelin ◽  
Katharina van Pee ◽  
Jochen Kuper ◽  
Caroline Kisker ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Complexes ◽  
Sm Proteins ◽  
Entropy Reduction ◽  
Multimeric Protein ◽  
Complex Project ◽  
Key Steps ◽  
Small Nuclear Ribonucleoproteins

The small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/6 and U5 are major constituents of the pre-mRNA processing spliceosome. They contain a common RNP core that is formed by the ordered binding of Sm proteins onto the single-stranded Sm site of the snRNA. Although spontaneousin vitro, assembly of the Sm core requires assistance from the PRMT5 and SMN complexesin vivo. To gain insight into the key steps of the assembly process, the crystal structures of two assembly intermediates of U snRNPs termed the 6S and 8S complexes have recently been reported. These multimeric protein complexes could only be crystallized after the application of various rescue strategies. The developed strategy leading to the crystallization and solution of the 8S crystal structure was subsequently used to guide a combination of rational crystal-contact optimization with surface-entropy reduction of crystals of the related 6S complex. Conversely, the resulting high-resolution 6S crystal structure was used during the restrained refinement of the 8S crystal structure.

scholarly journals Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

2021 ◽  
Author(s):  
Tim Neijenhuis ◽  
Siri C. van Keulen ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Protein Complexes ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Protein Interfaces ◽  
Density Maps ◽  
Medium Resolution ◽  
Wide Range ◽  
Multimeric Protein

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.

scholarly journals Insight Into Inflammasome Signaling: Implications for Toxoplasma gondii Infection

2020 ◽  
Vol 11 ◽  
Author(s):  
Yang Wang ◽  
Jinjin Zhu ◽  
Yuanyuan Cao ◽  
Jilong Shen ◽  
Li Yu
Keyword(s):  
Toxoplasma Gondii ◽  
Protein Complexes ◽  
Innate Immune ◽  
Leucine Rich Repeat ◽  
Proteolytic Activation ◽  
Obligate Intracellular ◽  
Obligate Intracellular Parasite ◽  
Multimeric Protein ◽  
Toxoplasma Gondii Infection ◽  
Insight Into

Inflammasomes are multimeric protein complexes regulating the innate immune response to invading pathogens or stress stimuli. Recent studies have reported that nucleotide-binding leucine-rich repeat-containing (NLRs) proteins and DNA sensor absent in melanoma 2 (AIM2) serve as inflammasome sentinels, whose stimulation leads to the proteolytic activation of caspase-1, proinflammatory cytokine secretion, and pyroptotic cell death. Toxoplasma gondii, an obligate intracellular parasite of phylum Apicomplexans, is reportedly involved in NLRP1, NLRP3 and AIM2 inflammasomes activation; however, mechanistic evidence regarding the activation of these complexes is preliminary. This review describes the current understanding of inflammasome signaling in rodent and human models of T. gondii infection.

Human NLRP1: From the shadows to center stage

2021 ◽  
Vol 219 (1) ◽  
Author(s):  
Stefan Bauernfried ◽  
Veit Hornung
Keyword(s):  
Cell Death ◽  
Host Defense ◽  
Essential Role ◽  
Protein Complexes ◽  
Cell Damage ◽  
Specific Cell ◽  
Multimeric Protein ◽  
Functional Relevance ◽  
Molecular Mode ◽  
Pro Inflammatory Cytokines

In response to infection or cell damage, inflammasomes form intracellular multimeric protein complexes that play an essential role in host defense. Activation results in the maturation and subsequent secretion of pro-inflammatory cytokines of the IL-1 family and a specific cell death coined pyroptosis. Human NLRP1 was the first inflammasome-forming sensor identified at the beginning of the millennium. However, its functional relevance and its mechanism of activation have remained obscure for many years. Recent discoveries in the NLRP1 field have propelled our understanding of the functional relevance and molecular mode of action of this unique inflammasome sensor, which we will discuss in this perspective.

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