Equilibrium studies of the reactions of palladium(ii) bis(imidazolin-2-imine) complexes with biologically relevant nucleophiles. The crystal structures of [(TLtBu)PdCl]ClO4 and [(BLiPr)PdCl2]

2011 ◽  
Vol 40 (24) ◽  
pp. 6515 ◽  
Author(s):  
Jovana Bogojeski ◽  
Ratomir Jelić ◽  
Dejan Petrović ◽  
Eberhardt Herdtweck ◽  
Peter G. Jones ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Equilibrium Studies ◽  
Biologically Relevant

scholarly journals The staphylococcal biofilm protein Aap forms a tetrameric species as a necessary intermediate before amyloidogenesis

2020 ◽  
Vol 295 (37) ◽  
pp. 12840-12850
Author(s):  
Alexander E. Yarawsky ◽  
Andrew B. Herr
Keyword(s):  
Staphylococcus Epidermidis ◽  
Analytical Ultracentrifugation ◽  
Conformational Transition ◽  
Mechanistic Model ◽  
Critical Factor ◽  
Equilibrium Studies ◽  
Dimer Interface ◽  
Biologically Relevant ◽  
Accumulation Associated Protein ◽  
Initial Assembly

The accumulation-associated protein (Aap) from Staphylococcus epidermidis is a biofilm-related protein that was found to be a critical factor for infection using a rat catheter model. The B-repeat superdomain of Aap, composed of 5–17 B-repeats, each containing a Zn2+-binding G5 and a spacer subdomain, is responsible for Zn2+-dependent assembly leading to accumulation of bacteria during biofilm formation. We previously demonstrated that a minimal B-repeat construct (Brpt1.5) forms an antiparallel dimer in the presence of 2–3 Zn2+ ions. More recently, we have reported the presence of functional amyloid-like fibrils composed of Aap within S. epidermidis biofilms and demonstrated that a biologically relevant construct containing five and a half B-repeats (Brpt5.5) forms amyloid-like fibrils similar to those observed in the biofilm. In this study, we analyze the initial assembly events of the Brpt5.5 construct. Analytical ultracentrifugation was utilized to determine hydrodynamic parameters of reversibly associating species and to perform linked equilibrium studies. Linkage studies indicated a mechanism of Zn2+-induced dimerization similar to smaller constructs; however, Brpt5.5 dimers could then undergo further Zn2+-induced assembly into a previously uncharacterized tetramer. This led us to search for potential Zn2+-binding sites outside of the dimer interface. We developed a Brpt5.5 mutant that was unable to form the tetramer and was concordantly incapable of amyloidogenesis. CD and dynamic light scattering indicate that a conformational transition in the tetramer species is a critical step preceding amyloidogenesis. This mechanistic model for B-repeat assembly and amyloidogenesis provides new avenues for potential therapeutic targeting of staphylococcal biofilms.

Synthesis and coordination properties of new macrocyclic ligands: equilibrium studies and crystal structures

2004 ◽  
pp. 3468 ◽  
Author(s):  
Gianluca Ambrosi ◽  
Paolo Dapporto ◽  
Mauro Formica ◽  
Vieri Fusi ◽  
Luca Giorgi ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Macrocyclic Ligands ◽  
Equilibrium Studies ◽  
Coordination Properties

scholarly journals Structural variability of CG-rich DNA 18-mers accommodating double T–T mismatches

2020 ◽  
Vol 76 (12) ◽  
pp. 1233-1243
Author(s):  
Petr Kolenko ◽  
Jakub Svoboda ◽  
Jiří Černý ◽  
Tatsiana Charnavets ◽  
Bohdan Schneider
Keyword(s):  
Crystal Structures ◽  
Bacterial Species ◽  
Crystal Data ◽  
Temperature Dependent ◽  
Base Pairs ◽  
Biologically Relevant ◽  
Dynamic Temperature ◽  
Dna Crystals ◽  
Helical Geometry ◽  
Work Knowledge

Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T–T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T–T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.

Cruciform structures and functions

1996 ◽  
Vol 29 (4) ◽  
pp. 279-307 ◽  
Author(s):  
Youri Timsit ◽  
Dino Moras
Keyword(s):  
High Resolution ◽  
Structure Function ◽  
Crystal Structures ◽  
Function Analysis ◽  
Dna Interactions ◽  
Biologically Relevant ◽  
Dna Molecule ◽  
Biological Importance ◽  
Crystal Packings

In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

scholarly journals The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

2021 ◽  
Author(s):  
Eva Estebanez-Perpiña ◽  
Alba Jimenez-Panizo ◽  
Andrea Alegre-Marti ◽  
Gregory Fettweis ◽  
Montserrat Abella ◽  
...  
Keyword(s):  
Glucocorticoid Receptor ◽  
Ligand Binding ◽  
Crystal Structures ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Oligomeric State ◽  
Biologically Relevant ◽  
Structural Work ◽  
Quantitative Fluorescence ◽  
Glucocorticoid Action

The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution and quantitative fluorescence microscopy in living cells. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work unveils likely pathophysiologically relevant quaternary assemblies of the nuclear receptor with important implications for glucocorticoid action and drug design.

scholarly journals Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality

2017 ◽  
Author(s):  
Julia Koehler Leman ◽  
Andrew R. D’Avino ◽  
Yash Bhatnagar ◽  
Jeffrey J. Gray
Keyword(s):  
Membrane Proteins ◽  
Crystal Structures ◽  
Protein Structures ◽  
Structural Quality ◽  
Model Quality ◽  
Biologically Relevant ◽  
X Ray Crystallography ◽  
Nmr Structures ◽  
Improve Model ◽  
Membrane Region

AbstractMembrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is “which structure is most biologically relevant?” Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.

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