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Nucleic Acids Research Jul 2021Protein-protein interactions play crucial roles in diverse biological processes, including various disease progressions. Atomistic structural details of protein-protein...
Protein-protein interactions play crucial roles in diverse biological processes, including various disease progressions. Atomistic structural details of protein-protein interactions may provide important information that can facilitate the design of therapeutic agents. GalaxyHeteromer is a freely available automatic web server (http://galaxy.seoklab.org/heteromer) that predicts protein heterodimer complex structures from two subunit protein sequences or structures. When subunit structures are unavailable, they are predicted by template- or distance-prediction-based modelling methods. Heterodimer complex structures can be predicted by both template-based and ab initio docking, depending on the template's availability. Structural templates are detected from the protein structure database based on both the sequence and structure similarities. The templates for heterodimers may be selected from monomer and homo-oligomer structures, as well as from hetero-oligomers, owing to the evolutionary relationships of heterodimers with domains of monomers or subunits of homo-oligomers. In addition, the server employs one of the best ab initio docking methods when heterodimer templates are unavailable. The multiple heterodimer structure models and the associated scores, which are provided by the web server, may be further examined by user to test or develop functional hypotheses or to design new functional molecules.
Topics: Molecular Docking Simulation; Protein Multimerization; Protein Subunits; Sequence Analysis, Protein; Software
PubMed: 34048578
DOI: 10.1093/nar/gkab422 -
Biological Chemistry Sep 2015The c ring of the Na+ F1F(o) ATP synthase from the anaerobic acetogenic bacterium Acetobacterium woodii is encoded by three different genes: atpE1, atpE2 and atpE3.... (Review)
Review
The c ring of the Na+ F1F(o) ATP synthase from the anaerobic acetogenic bacterium Acetobacterium woodii is encoded by three different genes: atpE1, atpE2 and atpE3. Subunit c1 is similar to typical V-type c subunits and has four transmembrane helices with one ion binding site. Subunit c2 and c3 are identical at the amino acid level and are typical F-type c subunits with one ion binding site in two transmembrane helices. All three constitute a hybrid F(o)V(o) c ring, the first found in nature. To analyze whether other species may have similar hybrid rotors, we searched every genome sequence publicly available as of 23 February 2015 for F1F(o) ATPase operons that have more than one gene encoding the c subunit. This revealed no other species that has three different c subunit encoding genes but twelve species that encode one F(o)- and one V(o)-type c subunit in one operon. Their c subunits have the conserved binding motif for Na+. The organisms are all anaerobic. The advantage of hybrid c rings for the organisms in their environments is discussed.
Topics: Acetobacterium; Amino Acid Sequence; Mitochondrial Proton-Translocating ATPases; Models, Molecular; Molecular Sequence Data; Protein Subunits; Sequence Alignment; Sodium
PubMed: 25838297
DOI: 10.1515/hsz-2015-0137 -
Biochimica Et Biophysica Acta Feb 2016ATP synthases (FoF1) are found ubiquitously in energy-transducing membranes of bacteria, mitochondria, and chloroplasts. These enzymes couple proton transport and ATP... (Review)
Review
ATP synthases (FoF1) are found ubiquitously in energy-transducing membranes of bacteria, mitochondria, and chloroplasts. These enzymes couple proton transport and ATP synthesis or hydrolysis through subunit rotation, which has been studied mainly by observing single molecules. In this review, we discuss the mechanism of rotational catalysis of ATP synthases, mainly that from Escherichia coli, emphasizing the high-speed and stochastic rotation including variable rates and an inhibited state. Single molecule studies combined with structural information of the bovine mitochondrial enzyme and mutational analysis have been informative as to an understanding of the catalytic site and the interaction between rotor and stator subunits. We discuss the similarity and difference in structure and inhibitory regulation of F1 from bovine and E. coli. Unlike the crystal structure of bovine F1 (α3β3γ), that of E. coli contains a ε subunit, which is a known inhibitor of bacterial and chloroplast F1 ATPases. The carboxyl terminal domain of E. coli ε (εCTD) interacts with the catalytic and rotor subunits (β and γ, respectively), and then inhibits rotation. The effects of phytopolyphenols on F1-ATPase are also discussed: one of them, piceatannol, lowered the rotational speed by affecting rotor/stator interactions.
Topics: Animals; Biocatalysis; Catalytic Domain; Cattle; Escherichia coli; Escherichia coli Proteins; Hydrolysis; Models, Molecular; Polyphenols; Protein Structure, Secondary; Protein Structure, Tertiary; Protein Subunits; Proton-Translocating ATPases; Rotation; Species Specificity; Thermodynamics
PubMed: 26589785
DOI: 10.1016/j.bbabio.2015.11.005 -
Proteins Dec 2021Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer...
Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human-expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain-splitting led to improved oligomeric domain structures by ab initio docking, automated oligomer structure refinement led to improved subunit orientation and terminal structure, and manual oligomer modeling utilizing literature information generated a reasonable oligomer model. We also discussed the results of post-prediction docking calculations with AlphaFold2 monomers as input in comparison to our blind prediction results. Overall, ab initio docking of AlphaFold2 models did not lead to better oligomer structure prediction, which may be attributed to the interfacial structural difference between the AlphaFold2 monomer structures and the crystal oligomer structures. This result poses a next-stage challenge in oligomer structure prediction after the success of AlphaFold2. For successful protein assembly structure prediction, a different approach that exploits further evolutionary information on the interface and/or flexible docking taking the interfacial conformational flexibilities of subunit structures into account is needed.
Topics: Computational Biology; Models, Molecular; Molecular Docking Simulation; Protein Conformation; Protein Folding; Protein Subunits; Proteins; Sequence Analysis, Protein; Software
PubMed: 34363243
DOI: 10.1002/prot.26203 -
Biochimica Et Biophysica Acta. Proteins... Mar 2019Chaperonin GroEL helps in the folding of substrate proteins under normal and stress conditions. Although it remains stable and functional during stress conditions, the...
Chaperonin GroEL helps in the folding of substrate proteins under normal and stress conditions. Although it remains stable and functional during stress conditions, the quantitative estimation of stability parameters and the specific amino-acid residues playing a role in its stability are not known in sufficient detail. The reason for poor understanding is its large size, multimeric nature, and irreversible unfolding process. The X-ray crystal structure reveals that equatorial domain forms almost all intra and inter-subunit interactions for assembly of GroEL. Considering all these facts, we adopted alternate strategies to use monomeric GroEL, native GroEL and equatorial domain mutants (GroEL/GroEL/GroEL) to study the assembly and stability of GroEL. Loss of inter-subunit interaction involving K4 residue of one subunit and E59, I60, E61, I62 residues of adjacent subunit due to K4E mutation affect the oligomerization efficiency of GroEL subunits while the equilibrium unfolding studies on wild-type monomeric GroEL, native GroEL, and the selected mutants together demonstrate that intra-subunit interactions involving K4 and D523 of the same subunit play a critical role in the thermodynamic stability of both native and monomeric GroEL without affecting the oligomerization of subunits. The stability order between the GroEL(M) and its variants is GroEL(M) ≥ GroEL(M)˃GroEL(M)˃GroEL.
Topics: Chaperonin 60; Protein Folding; Protein Stability; Protein Structure, Secondary; Protein Subunits; Temperature; Urea
PubMed: 30661519
DOI: 10.1016/j.bbapap.2018.10.012 -
Food Chemistry Dec 2023Prolyl endopeptidase can partially degrade soybean protein B subunit and alleviate soy sauce secondary precipitate. In this study, the influences of ultrasound-assisted...
Prolyl endopeptidase can partially degrade soybean protein B subunit and alleviate soy sauce secondary precipitate. In this study, the influences of ultrasound-assisted prolyl endopeptidase on the degradation of soybean protein B subunit of soy sauce and primary mechanism were investigated using SDS-PAGE, MALDI-TOF-MS, circular dichromatic spectrometer, fluorescence spectra, etc. Results showed that ultrasound-assisted prolyl endopeptidase enhanced 72% degradation rate of B subunit and reduced soy sauce secondary precipitate remarkably, meanwhile significantly increased content of organic taste compounds of soy sauce compared with control (p < 0.05). Sonication markedly reduced percentage of α-helix and increased percentage of random coil, made hydrophobic amino acids inside prolyl endopeptidase exposed to its surface and enhanced its flexibility, which facilitated the binding of prolyl endopeptidase active center with B subunit and finally enhanced the latter's degradation rate and appearance quality of soy sauce. This work laid a foundation for solving soy sauce secondary precipitate.
Topics: Soy Foods; Soybean Proteins; Prolyl Oligopeptidases; Molecular Weight; Protein Subunits; Fermentation; Protein Structure, Secondary; Sonication
PubMed: 37506662
DOI: 10.1016/j.foodchem.2023.136972 -
Journal of Chemical Information and... Mar 2018Protein complexes play deterministic roles in live entities in sensing, compiling, controlling, and responding to external and internal stimuli. Thermodynamic stability...
Protein complexes play deterministic roles in live entities in sensing, compiling, controlling, and responding to external and internal stimuli. Thermodynamic stability is an important property of protein complexes; having knowledge about complex stability helps us to understand the basics of protein assembly-related diseases and the mechanism of protein assembly clearly. Enormous protein-protein interactions, detected by high-throughput methods, necessitate finding fast methods for predicting the stability of protein assemblies in a quantitative and qualitative manner. The existing methods of predicting complex stability need knowledge about the three-dimensional (3D) structure of the intended protein complex. Here, we introduce a new method for predicting dissociation free energy of subunits by analyzing the structural and topological properties of a protein binding patch on a single subunit of the desired protein complex. The method needs the 3D structure of just one subunit and the information about the position of the intended binding site on the surface of that subunit to predict dimer stability in a classwise manner. The patterns of structural and topological properties of a protein binding patch are decoded by recurrence quantification analysis. Nonparametric discrimination is then utilized to predict the stability class of the intended dimer with accuracy greater than 85%.
Topics: Algorithms; Animals; Binding Sites; Computer Simulation; Databases, Protein; Humans; Models, Biological; Protein Conformation; Protein Multimerization; Protein Stability; Protein Subunits; Proteins; Thermodynamics
PubMed: 29444397
DOI: 10.1021/acs.jcim.7b00606 -
Trends in Biochemical Sciences Aug 2017The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the... (Review)
Review
The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the ordered assembly of ∼80 ribosomal proteins (r-proteins). Ribosome synthesis is catalyzed and coordinated by more than 200 biogenesis factors as the preribosomal subunits acquire maturity on their path from the nucleolus to the cytoplasm. Several biogenesis factors also interconnect the progression of ribosome assembly with quality control of important domains, ensuring that only functional subunits engage in translation. With the recent visualization of several assembly intermediates by cryoelectron microscopy (cryo-EM), a structural view of ribosome assembly begins to emerge. In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps.
Topics: Cryoelectron Microscopy; Nucleic Acid Conformation; Protein Subunits; Ribosomes
PubMed: 28579196
DOI: 10.1016/j.tibs.2017.05.005 -
Methods in Molecular Biology (Clifton,... 2020Saccharomyces cerevisiae is a useful eukaryotic expression system for mitochondrial membrane proteins due to its ease of growth and ability to provide a native membrane...
Saccharomyces cerevisiae is a useful eukaryotic expression system for mitochondrial membrane proteins due to its ease of growth and ability to provide a native membrane environment. The development of the pBEVY vector system has further increased the potential of S. cerevisiae as an expression system by creating a method for expressing multiple proteins simultaneously. This vector system is amenable to the expression and purification of multi-subunit protein complexes. Here we describe the cloning, yeast transformation, and co-expression of multi-subunit outer mitochondrial membrane complexes using the pBEVY vector system.
Topics: Cell Fractionation; Cloning, Molecular; Gene Expression Regulation, Fungal; Genetic Vectors; Membrane Proteins; Mitochondrial Membranes; Mitochondrial Proteins; Organisms, Genetically Modified; Protein Multimerization; Protein Processing, Post-Translational; Protein Subunits; Recombinant Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Transformation, Genetic
PubMed: 32112311
DOI: 10.1007/978-1-0716-0373-4_1 -
Zhejiang Da Xue Xue Bao. Yi Xue Ban =... Oct 2021The N-methyl-D-aspartate receptor (NMDAR) in central nerve system is mostly composed of GluN1 and GluN2 subunits. The classical NMDAR has been intensively studied.... (Review)
Review
The N-methyl-D-aspartate receptor (NMDAR) in central nerve system is mostly composed of GluN1 and GluN2 subunits. The classical NMDAR has been intensively studied. However, GluN3‑containing NMDAR is much less expressed and have atypical channel properties. Recently, accumulating evidences have revealed two types of GluN3‑containing NMDAR: glutamate-gated GluN1/GluN2/GluN3 NMDAR and glycine-gated GluN1/GluN3 NMDAR. The former may play important roles in regulating synapse maturation and pruning non-used synapses, and its elevated expression at the adult stage may alter synaptic reorganization in some neuropsychiatric disorders. The latter is expressed in the medial habenula and involves in control of aversion. This article reviews the recent progresses on the expression, functional properties of GluN3‑containing atypical NMDARs and the physiological and pathological relevance.
Topics: Central Nervous System; Protein Subunits; Receptors, N-Methyl-D-Aspartate; Synapses
PubMed: 34986531
DOI: 10.3724/zdxbyxb-2021-0167