scholarly journals Structural basis for 2′-deoxyguanosine recognition by the 2′-dG-II class of riboswitches

2019 ◽  
Vol 47 (20) ◽  
pp. 10931-10941 ◽  
Author(s):  
Michal M Matyjasik ◽  
Robert T Batey
Keyword(s):  
Ligand Binding ◽  
Consensus Sequence ◽  
Bioinformatic Analysis ◽  
Binding Pocket ◽  
Structural Basis ◽  
Binding Core ◽  
Nucleotide Insertion ◽  
Parental Class ◽  
Purine Riboswitch ◽  
Aptamer Domain

Abstract A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate from the consensus sequence at one or more of three positions directly involved purine nucleobase recognition, one of which was validated as a second class of 2′-deoxyguanosine riboswitch (called 2′-dG-II). To understand how 2′-dG-II riboswitches recognize their cognate ligand and how they differ from a previously identified class of 2′-deoxyguanosine binding riboswitches, we have solved the crystal structure of a 2′-dG-II aptamer domain bound to 2′-deoxyguanosine. This structure reveals a global architecture similar to other members of the purine riboswitch family, but contains key differences within the ligand binding core. Defining the 2′-dG-II riboswitches is a two-nucleotide insertion in the three-way junction that promotes novel base-base interactions. Unlike 2′-dG-I riboswitches, the 2′-dG-II class only requires local changes to the ligand binding pocket of the guanine/adenine class to achieve a change in ligand preference. Notably, members of the 2′-dG-II family have variable ability to discriminate between 2′-deoxyguanosine and riboguanosine, suggesting that a subset of 2′-dG-II riboswitches may bind either molecule to regulate gene expression.

scholarly journals Structural Basis for PPARs Activation by the Dual PPARα/γ Agonist Sanguinarine: A Unique Mode of Ligand Recognition

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 6012
Author(s):  
Siyu Tian ◽  
Rui Wang ◽  
Shuming Chen ◽  
Jialing He ◽  
Weili Zheng ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Target Genes ◽  
Binding Pocket ◽  
Binding Mode ◽  
Structural Basis ◽  
Peroxisome Proliferator ◽  
Functional Studies ◽  
Glucose And Lipid Metabolism ◽  
Peroxisome Proliferator Activated Receptors ◽  
Dual Agonist

Peroxisome proliferator-activated receptors (PPARs) play crucial roles in glucose and lipid metabolism and inflammation. Sanguinarine is a natural product that is isolated from Sanguinaria Canadensis, a potential therapeutic agent for intervention in chronic diseases. In this study, biochemical and cell-based promoter-reporter gene assays revealed that sanguinarine activated both PPARα and PPARγ, and enhanced their transcriptional activity; thus, sanguinarine was identified as a dual agonist of PPARα/γ. Similar to fenofibrate, sanguinarine upregulates the expression of PPARα-target genes in hepatocytes. Sanguinarine also modulates the expression of key PPARγ-target genes and promotes adipocyte differentiation, but with a lower adipogenic activity compared with rosiglitazone. We report the crystal structure of sanguinarine bound to PPARα, which reveals a unique ligand-binding mode of sanguinarine, dissimilar to the classic Y-shaped binding pocket, which may represent a new pharmacophore that can be optimized for selectively targeting PPARα. Further structural and functional studies uncover the molecular basis for the selectivity of sanguinarine toward PPARα/γ among all three PPARs. In summary, our study identifies a PPARα/γ dual agonist with a unique ligand-binding mode, and provides a promising and viable novel template for the design of dual-targeting PPARs ligands.

scholarly journals Rhodopsin: Structural Basis of Molecular Physiology

2001 ◽  
Vol 81 (4) ◽  
pp. 1659-1688 ◽  
Author(s):  
Santosh T. Menon ◽  
May Han ◽  
Thomas P. Sakmar
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Critical Evaluation ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Structural Basis ◽  
Molecular Physiology ◽  
Movement Model ◽  
Ligand Binding Pocket ◽  
Cytoplasmic Surface

The crystal structure of rod cell visual pigment rhodopsin was recently solved at 2.8-Å resolution. A critical evaluation of a decade of structure-function studies is now possible. It is also possible to begin to explain the structural basis for several unique physiological properties of the vertebrate visual system, including extremely low dark noise levels as well as high gain and color detection. The ligand-binding pocket of rhodopsin is remarkably compact, and several apparent chromophore-protein interactions were not predicted from extensive mutagenesis or spectroscopic studies. The transmembrane helices are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The helix movement model of receptor activation, which might apply to all G protein-coupled receptors (GPCRs) of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor is remarkable for a carboxy-terminal helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. Thus the cytoplasmic surface appears to be approximately the right size to bind to the transducin heterotrimer in a one-to-one complex. Future high-resolution structural studies of rhodopsin and other GPCRs will form a basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.

Critical residues for ligand binding in blade 2 of the propeller domain of the integrin αIIb subunit

2004 ◽  
Vol 91 (01) ◽  
pp. 111-118 ◽  
Author(s):  
Tatsushiro Tamura ◽  
Jun Yamanouchi ◽  
Shigeru Fujita ◽  
Takaaki Hato
Keyword(s):  
Crystal Structure ◽  
Ligand Binding ◽  
Binding Site ◽  
Thrombus Formation ◽  
Direct Interaction ◽  
Binding Pocket ◽  
Crystal Structure Analysis ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Critical Residues

SummaryLigand binding to integrin αIIbβ3 is a key event of thrombus formation. The propeller domain of the αIIb subunit has been implicated in ligand binding. Recently, the ligand binding site of the αV propeller was determined by crystal structure analysis. However, the structural basis of ligand recognition by the αIIb propeller remains to be determined. In this study, we conducted site-directed mutagenesis of all residues located in the loops extending above blades 2 and 4 of the αIIb propeller, which are spatially close to, but distinct from, the loops that contain the binding site for an RGD ligand in the crystal structure of the αV propeller. Replacement by alanine of Q111, H112 or N114 in the loop within the blade 2 (the W2:2-3 loop in the propeller model) abolished binding of a ligand-mimetic antibody and fibrinogen to αIIbβ3 induced by different types of integrin activation including activation of αIIbβ3 by β3 cytoplasmic mutation. CHO cells stably expressing recombinant αIIbβ3 bearing Q111A, H112A or N114A mutation did not exhibit αIIbβ3mediated adhesion to fibrinogen. According to the crystal structure of αVβ3, the αV residue corresponding to αIIbN114 is exposed on the integrin surface and close to the RGD binding site. These results suggest that the Q111, H112 and N114 residues in the loop within blade 2 of the αIIb propeller are critical for ligand binding, possibly because of direct interaction with ligands or modulation of the RGD binding pocket.

Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

2006 ◽  
Vol 359 (3) ◽  
pp. 754-768 ◽  
Author(s):  
Sunny D. Gilbert ◽  
Colby D Stoddard ◽  
Sarah J. Wise ◽  
Robert T. Batey
Keyword(s):  
Ligand Binding ◽  
Kinetic Characterization ◽  
Purine Riboswitch ◽  
Aptamer Domain

scholarly journals Structural Basis for Control of Bacterial RNA Polymerase Pausing by a Riboswitch and its Ligand

2021 ◽  
Author(s):  
Nils Walter ◽  
Adrien Chauvier ◽  
Jason Porta ◽  
Indrajit Deb ◽  
Emily Ellinger ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Rna Polymerase ◽  
Bound States ◽  
Consensus Sequence ◽  
Structural Basis ◽  
Helical Axis ◽  
Tight Coupling ◽  
Ligand Free ◽  
Nascent Rna ◽  
Polymerase Pausing

Abstract Folding of nascent transcripts can be modulated by the proximal RNA polymerase (RNAP) that carries out their transcription, and vice versa. A pause of RNAP during transcription of a preQ1 riboswitch (que-ePEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination, however, the mechanism by which riboswitch folding modulates pausing is unclear. Here, we report single-particle cryo-electron microscopy reconstructions of que-ePEC in ligand-free and ligand-bound states. In the absence of preQ1, the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Strikingly, upon ligand binding the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. Our study reveals the tight coupling by which small nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery.

scholarly journals Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch

2013 ◽  
Vol 425 (10) ◽  
pp. 1596-1611 ◽  
Author(s):  
Colby D. Stoddard ◽  
Jeremy Widmann ◽  
Jeremiah J. Trausch ◽  
Joan G. Marcano-Velázquez ◽  
Rob Knight ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Pocket ◽  
Ligand Binding Pocket ◽  
Purine Riboswitch

scholarly journals Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction

2018 ◽  
Vol 74 (4) ◽  
pp. 214-221 ◽  
Author(s):  
Kodai Hara ◽  
Masayuki Uchida ◽  
Risa Tagata ◽  
Hideshi Yokoyama ◽  
Yoshinobu Ishikawa ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Proliferating Cell Nuclear Antigen ◽  
Interaction Analysis ◽  
Consensus Sequence ◽  
Binding Pocket ◽  
Nuclear Antigen ◽  
Structural Basis ◽  
Protein Protein Interactions ◽  
Interacting Protein ◽  
Proliferating Cell

Proliferating cell nuclear antigen (PCNA) provides a molecular platform for numerous protein–protein interactions in DNA metabolism. A large number of proteins associated with PCNA have a well characterized sequence termed the PCNA-interacting protein box motif (PIPM). Another PCNA-interacting sequence termed the AlkB homologue 2 PCNA-interacting motif (APIM), comprising the five consensus residues (K/R)-(F/Y/W)-(L/I/V/A)-(L/I/V/A)-(K/R), has also been identified in various proteins. In contrast to that with PIPM, the PCNA–APIM interaction is less well understood. Here, the crystal structure of PCNA bound to a peptide carrying an APIM consensus sequence, RFLVK, was determined and structure-based interaction analysis was performed. The APIM peptide binds to the PIPM-binding pocket on PCNA in a similar way to PIPM. The phenylalanine and leucine residues within the APIM consensus sequence and a hydrophobic residue that precedes the APIM consensus sequence are crucially involved in interactions with the hydrophobic pocket of PCNA. This interaction is essential for overall binding. These results provide a structural basis for regulation of the PCNA interaction and might aid in the development of specific inhibitors of this interaction.

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