Metal ions induced secondary structure rearrangements: mechanically interlocked lassovs.unthreaded branched-cyclic topoisomers

The Analyst ◽  
2018 ◽  
Vol 143 (10) ◽  
pp. 2323-2333 ◽  
Author(s):  
Kevin Jeanne Dit Fouque ◽  
Javier Moreno ◽  
Julian D. Hegemann ◽  
Séverine Zirah ◽  
Sylvie Rebuffat ◽  
...  
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Metal Ions ◽  
Conformational Change ◽  
Structural Stability ◽  
Significant Role

Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change.

Diverse relationships between metal ions and the ribosome

2021 ◽  
Author(s):  
Genki Akanuma
Keyword(s):  
Gene Expression ◽  
Secondary Structure ◽  
Metal Ions ◽  
Structural Stability ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Cellular Homeostasis ◽  
Ribosomal Subunits ◽  
Translational Activity

Abstract The ribosome requires metal ions for structural stability and translational activity. These metal ions are important for stabilizing the secondary structure of ribosomal RNA, binding of ribosomal proteins to the ribosome, and for interaction of ribosomal subunits. In this review, various relationships between ribosomes and metal ions, especially Mg2+ and Zn2+, are presented. Mg2+ regulates gene expression by modulating the translational stability and synthesis of ribosomes, which in turn contribute to the cellular homeostasis of Mg2+. In addition, Mg2+ can partly complement the function of ribosomal proteins. Conversely, a reduction in the cellular concentration of Zn2+ induces replacement of ribosomal proteins, which mobilizes free-Zn2+ in the cell and represses translation activity. Evolutional relationships between these metal ions and the ribosome are also discussed.

Metal ions provide structural stability and compactness to tetrameric purothionin

RSC Advances ◽  
2016 ◽  
Vol 6 (93) ◽  
pp. 90690-90700 ◽  
Author(s):  
Swagata Das ◽  
Uttam Pal ◽  
Nakul Chandra Maiti
Keyword(s):  
Metal Ions ◽  
Structural Stability

Metal ions impart structural stability to the purothionin tetramer.

scholarly journals Speed limit of protein folding evidenced in secondary structure dynamics

2011 ◽  
Vol 108 (40) ◽  
pp. 16622-16627 ◽  
Author(s):  
M. M. Lin ◽  
O. F. Mohammed ◽  
G. S. Jas ◽  
A. H. Zewail
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Speed Limit ◽  
Structure Dynamics

scholarly journals Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1999 ◽  
Vol 32 (3) ◽  
pp. 241-284 ◽  
Author(s):  
William G. Scott
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Large Scale ◽  
Enzyme Inhibitor ◽  
Hammerhead Ribozyme ◽  
Three Dimensional ◽  
Chemical Mechanism ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hammerhead Rna

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

Backbone dihedral angles prediction servers for protein early-stage structure prediction

2019 ◽  
Vol 15 (4) ◽  
Author(s):  
Tomasz Smolarczyk ◽  
Katarzyna Stapor ◽  
Irena Roterman-Konieczna
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Protein Function ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Early Stage ◽  
Three Dimensional ◽  
Stage Structure ◽  
Dihedral Angles ◽  
Starting Point

AbstractThree-dimensional protein structure prediction is an important task in science at the intersection of biology, chemistry, and informatics, and it is crucial for determining the protein function. In the two-stage protein folding model, based on an early- and late-stage intermediates, we propose to use state-of-the-art secondary structure prediction servers for backbone dihedral angles prediction and devise an early-stage structure. Early-stage structures are used as a starting point for protein folding simulations, and any errors in this stage affect the final predictions. We have shown that modern secondary structure prediction servers could increase the accuracy of early-stage predictions compared to previously reported models.

scholarly journals Effects of zinc and other metal ions on the stability and activity of Escherichia coli alkaline phosphatase

1971 ◽  
Vol 124 (1) ◽  
pp. 25-30 ◽  
Author(s):  
C. N. A. Trotman ◽  
C. Greenwood
Keyword(s):  
Escherichia Coli ◽  
Alkaline Phosphatase ◽  
Metal Ions ◽  
Phosphatase Activity ◽  
Structural Stability ◽  
Zinc Content ◽  
Sedimentation Velocity ◽  
Reducing Agent ◽  
Deficient Mutant ◽  
The Stability

Measurement of the ultraviolet circular dichroism of apo-(alkaline phosphatase) in urea solutions showed substantial denaturation in 3m-urea. A zinc-deficient mutant alkaline phosphatase behaved similarly. The stability of the enzyme in 6m-urea was followed as a function of its zinc content and was found to be dependent on the first two of the four zinc atoms bound by apoenzyme. Phosphatase activity was mostly dependent on a second pair of zinc atoms. Mn2+, Co2+, Cu2+ or Cd2+ also restored structural stability. Sedimentation-velocity and -equilibrium experiments revealed that dissociation of the dimer accompanied apoenzyme denaturation in urea concentrations of 1m or higher, without treatment with disulphide-reducing agent.

scholarly journals Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper

2015 ◽  
Vol 6 (12) ◽  
pp. 7311-7318 ◽  
Author(s):  
Claudia Poloni ◽  
Marc C. A. Stuart ◽  
Pieter van der Meulen ◽  
Wiktor Szymanski ◽  
Ben L. Feringa
Keyword(s):  
Secondary Structure ◽  
Conformational Change ◽  
Fiber Formation ◽  
Major Influence ◽  
Heat Control ◽  
Large Conformational Change

The use of an overcrowded alkene photoswitch to control a model β-hairpin peptide is described. The light-induced, large conformational change has major influence on the secondary structure and the aggregation of the peptide, permitting the triggered formation of amyloid-like fibrils.

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