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Biomolecules Nov 2020The bacterial RNA polymerase (RNAP) is a multi-subunit protein complex (α2ββ'ω σ) containing the smallest subunit, ω. Although identified early in RNAP research,... (Review)
Review
The bacterial RNA polymerase (RNAP) is a multi-subunit protein complex (α2ββ'ω σ) containing the smallest subunit, ω. Although identified early in RNAP research, its function remained ambiguous and shrouded with controversy for a considerable period. It was shown before that the protein has a structural role in maintaining the conformation of the largest subunit, β', and its recruitment in the enzyme assembly. Despite evolutionary conservation of ω and its role in the assembly of RNAP, mutants lacking (codes for ω) are viable due to the association of the global chaperone protein GroEL with RNAP. To get a better insight into the structure and functional role of ω during transcription, several dominant lethal mutants of ω were isolated. The mutants showed higher binding affinity compared to that of native ω to the α2ββ' subassembly. We observed that the interaction between α2ββ' and these lethal mutants is driven by mostly favorable enthalpy and a small but unfavorable negative entropy term. However, during the isolation of these mutants we isolated a silent mutant serendipitously, which showed a lethal phenotype. Silent mutant of a given protein is defined as a protein having the same sequence of amino acids as that of wild type but having mutation in the gene with alteration in base sequence from more frequent code to less frequent one due to codon degeneracy. Eventually, many silent mutants were generated to understand the role of rare codons at various positions in . We observed that the dominant lethal mutants of ω having either point mutation or silent in nature are more structured in comparison to the native ω. However, the silent code's position in the reading frame of plays a role in the structural alteration of the translated protein. This structural alteration in ω makes it more rigid, which affects the plasticity of the interacting domain formed by ω and α2ββ'. Here, we attempted to describe how the conformational flexibility of the ω helps in maintaining the plasticity of the active site of RNA polymerase. The dominant lethal mutant of ω has a suppressor mapped near the catalytic center of the β' subunit, and it is the same for both types of mutants.
Topics: Bacterial Proteins; DNA-Directed RNA Polymerases; Mutant Proteins; Protein Subunits; Structure-Activity Relationship; Transcription Factors
PubMed: 33238579
DOI: 10.3390/biom10111588 -
EMBO Molecular Medicine Feb 2023The Elongator complex was initially identified in yeast, and a variety of distinct cellular functions have been assigned to the complex. In the last decade, several... (Review)
Review
The Elongator complex was initially identified in yeast, and a variety of distinct cellular functions have been assigned to the complex. In the last decade, several research groups focussed on dissecting its structure, tRNA modification activity and role in translation regulation. Recently, Elongator emerged as a crucial factor for various human diseases, and its involvement has triggered a strong interest in the complex from numerous clinical groups. The Elongator complex is highly conserved among eukaryotes, with all six subunits (Elp1-6) contributing to its stability and function. Yet, recent studies have shown that the two subcomplexes, namely the catalytic Elp123 and accessory Elp456, may have distinct roles in the development of different neuronal subtypes. This Commentary aims to provide a brief overview and new perspectives for more systematic efforts to explore the functions of the Elongator in health and disease.
Topics: Humans; Protein Subunits; Saccharomyces cerevisiae
PubMed: 36448458
DOI: 10.15252/emmm.202216418 -
International Journal of Molecular... Sep 2021Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5' end of precursor tRNAs (pre-tRNAs). In all organisms, the... (Review)
Review
Ribonuclease P (RNase P) is an important ribonucleoprotein (RNP), responsible for the maturation of the 5' end of precursor tRNAs (pre-tRNAs). In all organisms, the cleavage activity of a single phosphodiester bond adjacent to the first nucleotide of the acceptor stem is indispensable for cell viability and lies within an essential catalytic RNA subunit. Although RNase P is a ribozyme, its kinetic efficiency in vivo, as well as its structural variability and complexity throughout evolution, requires the presence of one protein subunit in bacteria to several protein partners in archaea and eukaryotes. Moreover, the existence of protein-only RNase P (PRORP) enzymes in several organisms and organelles suggests a more complex evolutionary timeline than previously thought. Recent detailed structures of bacterial, archaeal, human and mitochondrial RNase P complexes suggest that, although apparently dissimilar enzymes, they all recognize pre-tRNAs through conserved interactions. Interestingly, individual protein subunits of the human nuclear and mitochondrial holoenzymes have additional functions and contribute to a dynamic network of elaborate interactions and cellular processes. Herein, we summarize the role of each RNase P subunit with a focus on the human nuclear RNP and its putative role in flawless gene expression in light of recent structural studies.
Topics: Animals; Catalytic Domain; Humans; Kinetics; Protein Subunits; RNA Precursors; RNA, Catalytic; Ribonuclease P
PubMed: 34638646
DOI: 10.3390/ijms221910307 -
Nature Jun 2021AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR...
AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1-GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties.
Topics: Amino Acid Sequence; Animals; Calcium Channels; Cryoelectron Microscopy; Hippocampus; Ion Channel Gating; Lipid Metabolism; Lipids; Mice; Mice, Inbred C57BL; Models, Molecular; Protein Multimerization; Protein Subunits; Pyramidal Cells; Receptors, AMPA; Rotation
PubMed: 34079129
DOI: 10.1038/s41586-021-03613-0 -
The Journal of Physiology Jan 2022Non-conventional N-methyl-d-aspartate receptors (NMDARs) containing GluN3A subunits have unique biophysical, signalling and localization properties within the NMDAR... (Review)
Review
Non-conventional N-methyl-d-aspartate receptors (NMDARs) containing GluN3A subunits have unique biophysical, signalling and localization properties within the NMDAR family, and are typically thought to counterbalance functions of classical NMDARs made up of GluN1/2 subunits. Beyond their recognized roles in synapse refinement during postnatal development, recent evidence is building a wider perspective for GluN3A functions. Here we draw particular attention to the latest developments for this multifaceted and unusual subunit: from finely timed expression patterns that correlate with plasticity windows in developing brains or functional hierarchies in the mature brain to new insight onto presynaptic GluN3A-NMDARs, excitatory glycine receptors and behavioural impacts, alongside further connections to a range of brain disorders.
Topics: Protein Subunits; Receptors, Glycine; Receptors, N-Methyl-D-Aspartate; Signal Transduction; Synapses
PubMed: 33942912
DOI: 10.1113/JP280879 -
Scientific Reports Feb 2021The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as...
The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein-using its complete homo-trimer configuration with 2905 residues-our method identifies a large-scale opening and closing of the S1 subunit through movement of the S[Formula: see text] domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.
Topics: Antiviral Agents; Binding Sites; COVID-19; Crystallography, X-Ray; Drug Development; Humans; Models, Molecular; Pandemics; Protein Binding; Protein Domains; Protein Multimerization; Protein Subunits; SARS-CoV-2; Spike Glycoprotein, Coronavirus; COVID-19 Drug Treatment
PubMed: 33608565
DOI: 10.1038/s41598-021-82849-2 -
Cellular and Molecular Neurobiology Jan 2021Nicotinic acetylcholine receptors (nAChRs) have gained much attention in the scientific community since they play a significant role in multiple physiological and... (Review)
Review
Nicotinic acetylcholine receptors (nAChRs) have gained much attention in the scientific community since they play a significant role in multiple physiological and pathophysiological processes. Multiple approaches to study the receptors exist, with characterization of the receptors' functionality at a single cellular level using cell culturing being one of them. Derived from an adrenal medulla tumor, PC12 cells express nicotinic receptor subunits and form functional nicotinic receptors. Thus, the cells offer a convenient environment to address questions related to the functionality of the receptors. The review summarizes the findings on nicotinic receptors' expression and functions which were conducted using PC12 cells. Specific focus is given to α3-containing receptors as well as α7 receptor. Critical evaluation of findings is provided alongside insights into what can still be learned about nAChRs, using PC12 cells.
Topics: Animals; Models, Biological; PC12 Cells; Protein Subunits; Rats; Receptors, Nicotinic
PubMed: 32335772
DOI: 10.1007/s10571-020-00846-x -
Biochimica Et Biophysica Acta.... Apr 2020Photosynthesis is a fundamental biological process involving the conversion of solar energy into chemical energy. The initial photochemical and photophysical events of... (Comparative Study)
Comparative Study Review
Photosynthesis is a fundamental biological process involving the conversion of solar energy into chemical energy. The initial photochemical and photophysical events of photosynthesis are mediated by photosystem II (PSII) and photosystem I (PSI). Both PSII and PSI are multi-subunit supramolecular machineries composed of a core complex and a peripheral antenna system. The antenna system serves to capture light energy and transfer it to the core efficiently. Both PSII and PSI in the green lineage (plants and green algae) and PSI in red algae have an antenna system comprising a series of chlorophyll- and carotenoid-binding membrane proteins belonging to the light-harvesting complex (LHC) superfamily, including LHCII and LHCI. However, the antenna size and subunit composition vary considerably in the two photosystems from diverse organisms. On the basis of the plant and algal LHCII and LHCI structures that have been solved by X-ray crystallography and single-particle cryo-electron microscopy we review the detailed structural features and characteristic pigment properties of these LHCs in PSII and PSI. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.
Topics: Amino Acid Sequence; Apoproteins; Chlamydomonas reinhardtii; Chlorophyll; Light-Harvesting Protein Complexes; Models, Molecular; Photosystem I Protein Complex; Photosystem II Protein Complex; Protein Subunits; Rhodophyta
PubMed: 31229568
DOI: 10.1016/j.bbabio.2019.06.010 -
Expert Review of Vaccines 2023Vaccines prevent disease and disability; save lives and represent a good assessment of health interventions. Several systematic reviews on the efficacy and effectiveness...
INTRODUCTION
Vaccines prevent disease and disability; save lives and represent a good assessment of health interventions. Several systematic reviews on the efficacy and effectiveness of COVID-19 vaccines have been published, but the immunogenicity and safety of these vaccines should also be addressed.
AREAS COVERED
This systemic investigation sought to explain the efficacy, immunogenicity, and safety of new vaccination technologies against SARS-CoV-2 in people over 18 years old. Original research studying the effectiveness on mRNA, protein subunit vaccines, and viral vector vaccines against SARS-CoV-2 in people over 18 years old was analyzed. Several databases (Web of Science, Scopus, MEDLINE and EMBASE) were searched between 2012 and November 2022 for English-language papers using text and MeSH terms related to SARS-CoV-2, mechanism, protein subunit vaccine, viral vector, and mRNA. The protocol was registered on PROSPERO, CRD42022341952. Study quality was assessed using the NICE methodology. We looked at a total of six original articles. All studies gathered and presented quantitative data.
EXPERT OPINION
Our results suggest that new vaccinations could have more than 90% efficacy against SARS-CoV-2, regardless of the technology used. Furthermore, adverse reactions go from mild to moderate, and good immunogenicity can be observed for all vaccine types.
Topics: Humans; Adolescent; Viral Vaccines; Protein Subunits; COVID-19 Vaccines; SARS-CoV-2; RNA, Messenger; COVID-19; Vaccines, Subunit; Antibodies, Viral; Immunogenicity, Vaccine
PubMed: 36484136
DOI: 10.1080/14760584.2023.2156861 -
Scientific Reports May 2023The optimal booster vaccine schedule against COVID-19 is still being explored. The present study aimed at assessment of the immunogenicity and antibody persistency of...
The optimal booster vaccine schedule against COVID-19 is still being explored. The present study aimed at assessment of the immunogenicity and antibody persistency of inactivated-virus based vaccine, BBIP-CorV and protein-subunit based vaccines, PastoCovac/Plus through heterologous and homologous prime-boost vaccination. Totally, 214 individuals who were previously primed with BBIBP-CorV vaccines were divided into three arms on their choice as heterologous regimens BBIBP-CorV/PastoCovac (n = 68), BBIBP-CorV/PastoCovac Plus (n = 72) and homologous BBIBP-CorV (n = 74). PastoCovac booster recipients achieved the highest rate of anti-Spike IgG titer rise with a fourfold rise in 50% of the group. Anti-RBD IgG and neutralizing antibody mean rise and fold rise were almost similar between the PastoCovac and PastoCovac Plus booster receivers. The antibody durability results indicated that the generated antibodies were persistent until day 180 in all three groups. Nevertheless, a higher rate of antibody titer was seen in the heterologous regimen compared to BBIP-CorV group. Furthermore, no serious adverse event was recorded. The protein subunit-based booster led to a stronger humoral immune response in comparison with the BBIP-CorV booster receivers. Both the protein subunit boosters neutralized SARS-CoV-2 significantly more than BBIP-CorV. Notably, PastoCovac protein subunit-based vaccine could be successfully applied as a booster with convenient immunogenicity and safety profile.
Topics: Humans; COVID-19 Vaccines; Immunity, Humoral; Protein Subunits; COVID-19; SARS-CoV-2; Antibodies, Neutralizing; Immunoglobulin G; Antibodies, Viral
PubMed: 37202438
DOI: 10.1038/s41598-023-35147-y