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Protein Science : a Publication of the... Nov 2023Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of...
Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The x-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.
Topics: Periplasmic Binding Proteins; Carrier Proteins; Amino Acid Sequence; Ligands; Protein Binding; Evolution, Molecular
PubMed: 37788980
DOI: 10.1002/pro.4793 -
BMC Veterinary Research Jan 2024Poly C Binding Protein 1 (PCBP1) belongs to the heterogeneous nuclear ribonucleoprotein family. It is a multifunctional protein that participates in several functional...
BACKGROUND
Poly C Binding Protein 1 (PCBP1) belongs to the heterogeneous nuclear ribonucleoprotein family. It is a multifunctional protein that participates in several functional circuits and plays a variety of roles in cellular processes. Although PCBP1 has been identified in several mammals, its function in porcine was unclear.
RESULTS
In this study, we cloned the gene of porcine PCBP1 and analyzed its evolutionary relationships among different species. We found porcine PCBP1 protein sequence was similar to that of other animals. The subcellular localization of PCBP1 in porcine kidney cells 15 (PK-15) cells was analyzed by immunofluorescence assay (IFA) and revealed that PCBP1 was mainly localized to the nucleus. Reverse transcription-quantitative PCR (RT-qPCR) was used to compare PCBP1 mRNA levels in different tissues of 30-day-old pigs. Results indicated that PCBP1 was expressed in various tissues and was most abundant in the liver. Finally, the effects of PCBP1 on cell cycle and apoptosis were investigated following its overexpression or knockdown in PK-15 cells. The findings demonstrated that PCBP1 knockdown arrested cell cycle in G0/G1 phase, and enhanced cell apoptosis.
CONCLUSIONS
Porcine PCBP1 is a highly conserved protein, plays an important role in determining cell fate, and its functions need further study.
Topics: Swine; Animals; Carrier Proteins; RNA-Binding Proteins; DNA-Binding Proteins; Heterogeneous-Nuclear Ribonucleoproteins; Apoptosis; Protein Binding; Mammals
PubMed: 38218813
DOI: 10.1186/s12917-023-03861-4 -
Journal of Biomedicine & Biotechnology 2010Myosin binding protein C (MyBP-C) consists of a family of thick filament associated proteins. Three isoforms of MyBP-C exist in striated muscles: cardiac, slow skeletal,... (Review)
Review
Myosin binding protein C (MyBP-C) consists of a family of thick filament associated proteins. Three isoforms of MyBP-C exist in striated muscles: cardiac, slow skeletal, and fast skeletal. To date, most studies have focused on the cardiac form, due to its direct involvement in the development of hypertrophic cardiomyopathy. Here we focus on the slow skeletal form, discuss past and current literature, and present evidence to support that: (i) MyBP-C slow comprises a subfamily of four proteins, resulting from complex alternative shuffling of the single MyBP-C slow gene, (ii) the four MyBP-C slow isoforms are expressed in variable amounts in different skeletal muscles, (iii) at least one MyBP-C slow isoform is preferentially found at the periphery of M-bands and (iv) the MyBP-C slow subfamily may play important roles in the assembly and stabilization of sarcomeric M- and A-bands and regulate the contractile properties of the actomyosin filaments.
Topics: Animals; Carrier Proteins; Humans; Protein Isoforms
PubMed: 20396395
DOI: 10.1155/2010/652065 -
Scientific Reports Apr 2018The Y-box proteins are multifunctional nucleic acid-binding proteins involved in various aspects of gene regulation. The founding member of the Y-box protein family,...
The Y-box proteins are multifunctional nucleic acid-binding proteins involved in various aspects of gene regulation. The founding member of the Y-box protein family, YB-1, functions as a transcription factor as well as a principal component of messenger ribonucleoprotein particles (mRNPs) in somatic cells. The nuclear level of YB-1 is well correlated with poor prognosis in many human cancers. Previously, we showed that a Y-box protein-associated acidic protein, YBAP1, which is identical to complement component 1, q subcomponent-binding protein (C1QBP, also called gC1qR, hyaluronan-binding protein 1 [HABP1] or ASF/SF2-associated protein p32), relieves translational repression by YB-1. Here we show that the nuclear localization of YB-1 harboring a point mutation in the cold shock domain was inhibited when co-expressed with YBAP1, whereas cytoplasmic accumulation of the wild-type YB-1 was not affected. We showed that YBAP1 inhibited the interaction between YB-1 and transportin 1. In the cytoplasm, YBAP1 affected the accumulation of YB-1 to processing bodies (P-bodies) and partially abrogated the mRNA stabilization by YB-1. Our results, indicating that YBAP1/C1QBP regulates the nucleo-cytoplasmic distribution of YB-1 and its cytoplasmic functions, are consistent with a model that YBAP1/C1QBP acts as an mRNP remodeling factor.
Topics: Carrier Proteins; Cell Nucleus; Cytoplasm; Gene Expression; HeLa Cells; Humans; Mitochondrial Proteins; Models, Biological; Mutation; Protein Binding; Protein Interaction Domains and Motifs; Protein Transport; RNA Stability; RNA, Messenger; Y-Box-Binding Protein 1; beta Karyopherins
PubMed: 29670170
DOI: 10.1038/s41598-018-24401-3 -
The Journal of Biological Chemistry May 1981A binding protein from liver which binds reversibly to yeast mannan depending on the presence or absence of calcium has been purified to near homogeneity by affinity...
A binding protein from liver which binds reversibly to yeast mannan depending on the presence or absence of calcium has been purified to near homogeneity by affinity chromatography. The binding of the isolated protein to 125I-mannan is proportional to protein concentration and is apparently an unsaturable process. The Scatchard plot of the binding is a curvilinear, indicating the presence of a high affinity binding site with a dissociation constant of 1.62 X 10(-8) M. Evidence is presented to show that the protein recognizes and binds mannose and N-acetylglucosamine residues almost indiscriminately at the same binding site. Physical and chemical studies suggest the intact binding protein with an approximate molecular weight of 194,000 to be composed of six identical subunits. The protein is characterized as a glycine-rich protein. The apparent ubiquitous distribution of mannan-binding protein in mammalian liver is consistent with the proposal that the binding protein is the cellular receptor mediating the hepatic uptake of glycoproteins terminated with mannose and/or N-acetylglucosamine residues.
Topics: Amino Acids; Animals; Binding, Competitive; Carrier Proteins; Collectins; Electrophoresis, Polyacrylamide Gel; Hydrogen-Ion Concentration; Kinetics; Liver; Mannans; Polysaccharides; Rats; Saccharomyces cerevisiae
PubMed: 7012150
DOI: No ID Found -
FEBS Letters Jul 2016Polyglutamine tract-binding protein 1 (PQBP1) is an intrinsically disordered protein composed of a small folded WW domain and a long disordered region. PQBP1 binds to...
Polyglutamine tract-binding protein 1 (PQBP1) is an intrinsically disordered protein composed of a small folded WW domain and a long disordered region. PQBP1 binds to spliceosomal proteins WBP11 and U5-15kD through its N-terminal WW domain and C-terminal region, respectively. Here, we reveal that the binding between PQBP1 and WBP11 reduces the binding affinity between PQBP1 and U5-15kD. Our results suggest that the interaction between PQBP1 and WBP11 negatively modulates the U5-15kD binding of PQBP1 by an allosteric mechanism.
Topics: Allosteric Regulation; Carrier Proteins; DNA-Binding Proteins; Humans; Nuclear Proteins; Protein Binding; Protein Domains; RNA Splicing Factors; Ribonucleoprotein, U5 Small Nuclear
PubMed: 27314904
DOI: 10.1002/1873-3468.12256 -
Acta Crystallographica. Section D,... Jan 2023Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study...
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer-dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.
Topics: Carrier Proteins; Ribose; Proteins; Periplasmic Binding Proteins; Molecular Conformation; Bacterial Proteins
PubMed: 36601806
DOI: 10.1107/S205979832201186X -
Nature Structural & Molecular Biology Jul 2018Dynamic protein interaction networks such as DNA double-strand break (DSB) signaling are modulated by post-translational modifications. The DNA repair factor 53BP1 is a...
Dynamic protein interaction networks such as DNA double-strand break (DSB) signaling are modulated by post-translational modifications. The DNA repair factor 53BP1 is a rare example of a protein whose post-translational modification-binding function can be switched on and off. 53BP1 is recruited to DSBs by recognizing histone lysine methylation within chromatin, an activity directly inhibited by the 53BP1-binding protein TIRR. X-ray crystal structures of TIRR and a designer protein bound to 53BP1 now reveal a unique regulatory mechanism in which an intricate binding area centered on an essential TIRR arginine residue blocks the methylated-chromatin-binding surface of 53BP1. A 53BP1 separation-of-function mutation that abolishes TIRR-mediated regulation in cells renders 53BP1 hyperactive in response to DSBs, highlighting the key inhibitory function of TIRR. This 53BP1 inhibition is relieved by TIRR-interacting RNA molecules, providing proof-of-principle of RNA-triggered 53BP1 recruitment to DSBs.
Topics: Amino Acid Substitution; Binding Sites; Carrier Proteins; Crystallography, X-Ray; DNA Breaks, Double-Stranded; DNA Repair; Histones; Humans; Models, Molecular; Mutagenesis, Site-Directed; Protein Binding; Protein Engineering; Protein Interaction Maps; Protein Processing, Post-Translational; Pyrophosphatases; RNA-Binding Proteins; Tumor Suppressor p53-Binding Protein 1
PubMed: 29967538
DOI: 10.1038/s41594-018-0083-z -
FEBS Letters Sep 2021Substrate-binding proteins (SBPs) mediate ligand translocation and have been classified into seven clusters (A-G). Although the substrate specificities of these clusters...
Substrate-binding proteins (SBPs) mediate ligand translocation and have been classified into seven clusters (A-G). Although the substrate specificities of these clusters are known to some extent, their ligand-binding mechanism(s) remain(s) incompletely understood. In this study, the list of SBPs belonging to different clusters was updated (764 SBPs) compared to the previously reported study (504 SBPs). Furthermore, a new cluster referred to as cluster H was identified. Results reveal that SBPs follow different ligand-binding mechanisms. Intriguingly, the majority of the SBPs follow the 'one domain movement' rather than the well-known 'Venus Fly-trap' mechanism. Moreover, SBPs of a few clusters display subdomain conformational movement rather than the complete movement of the N- and C-terminal domains.
Topics: Carrier Proteins; Databases, Protein; Humans; Ligands; Models, Molecular; Movement; Protein Binding; Protein Domains; Protein Folding; Substrate Specificity
PubMed: 34379808
DOI: 10.1002/1873-3468.14174 -
The Journal of Biological Chemistry Sep 1991A novel Mr 17,000 heparin-binding protein was purified from culture medium conditioned by A431 human epidermoid carcinoma cells. This protein, designated HBp17, was...
A novel Mr 17,000 heparin-binding protein was purified from culture medium conditioned by A431 human epidermoid carcinoma cells. This protein, designated HBp17, was found to bind the heparin-binding peptide growth factors HBGF-1 and HBGF-2 in a noncovalent, reversible manner. In addition HBp17 was found to inhibit the biological activities of both HBGF-1 and HBGF-2. Both the binding and inactivation of HBGF-1 and HBGF-2 by HBp17 were abolished by heparin. Full-length 1163-base pair HBp17 cDNA was cloned and sequenced by using the polymerase chain reaction technique. The deduced primary structure of HBp17 consisted of 234 amino acids including each of five partial peptide sequences obtained from proteolytic fragments of purified HBp17. The encoded protein included a 33-residue N-terminal signal sequence for secretion and a single potential N-linked glycosylation site. No homology with any known protein was found for the deduced primary structure of HBp17. The expression of HBp17 mRNA was found to occur preferentially in normal human keratinocytes and in squamous cell carcinomas. This pattern of HBp17 gene expression suggests that this binding protein for HBGFs 1 and 2 has a physiological role in squamous epithelia.
Topics: Amino Acid Sequence; Base Sequence; Blotting, Northern; Blotting, Western; Carrier Proteins; Chromatography, Affinity; Cloning, Molecular; DNA; Heparin; Humans; Intercellular Signaling Peptides and Proteins; Molecular Sequence Data; Polymerase Chain Reaction; Tumor Cells, Cultured
PubMed: 1885605
DOI: No ID Found