scholarly journals Computational approaches for de novo design and redesign of metal-binding sites on proteins

2017 ◽  
Vol 37 (2) ◽  
Author(s):  
Gunseli Bayram Akcapinar ◽  
Osman Ugur Sezerman
Keyword(s):  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
De Novo ◽  
De Novo Design ◽  
Ion Binding ◽  
Chemical Transformations ◽  
Metal Ion Binding ◽  
Metal Binding Sites

Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.

Metal Ion Binding Properties of Perfluorosulfonate Membranes by Laser Excitation Spectroscopy

1988 ◽  
Vol 42 (2) ◽  
pp. 293-295 ◽  
Author(s):  
E. K. L. Wong ◽  
G. L. Richmond
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Laser Excitation ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Binding Properties ◽  
Metal Binding Sites ◽  
Fluorescence Measurements ◽  
Experimental Parameters

The metal ion binding properties of the perfluorosulfonate membrane Nafion® have been investigated in this study. The experiments involve laser-induced fluorescence measurements of europium (III) ions which are bound to the membrane. By the exploitation of the hypersensitivity of the D → F transitions of europium (III) to the ligand binding environment, the properties of the metal binding sites have been analyzed as a function of various experimental parameters. The spectra and fluorescence lifetime measurements provide evidence for distinct metal binding sites within the polymer, each of which is sensitive to the conditions of the membrane preparation.

The influence of metal-ion binding on the structure and surface composition of Sonic Hedgehog: a combined classical and hybrid QM/MM MD study

2016 ◽  
Vol 18 (32) ◽  
pp. 22254-22265 ◽  
Author(s):  
Manuel Hitzenberger ◽  
Thomas S. Hofer
Keyword(s):  
Metal Ions ◽  
Sonic Hedgehog ◽  
Binding Sites ◽  
Metal Ion ◽  
Surface Composition ◽  
Quantum Mechanical ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Structural Impact

The interaction of metal ions with Shh binding-sites and their structural impact are assessed via classical and quantum mechanical simulations.

scholarly journals Investigation of the nature of the two metal-binding sites in 5-aminolaevulinic acid dehydratase from Escherichia coli

1994 ◽  
Vol 300 (2) ◽  
pp. 373-381 ◽  
Author(s):  
P Spencer ◽  
P M Jordan
Keyword(s):  
Escherichia Coli ◽  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Fluorescence ◽  
Metal Binding Sites ◽  
Aminolaevulinic Acid ◽  
Acid Dehydratase ◽  
Aminolaevulinic Acid Dehydratase

Two distinct metal-binding sites, termed alpha and beta, have been characterized in 5-aminolaevulinic acid dehydratase from Escherichia coli. The alpha-site binds a Zn2+ ion that is essential for catalytic activity. This site can also utilize other metal ions able to function as a Lewis acid in the reaction mechanism, such as Mg2+ or Co2+. The beta-site is exclusively a transition-metal-ion-binding site thought to be involved in protein conformation, although a metal bound at this site only appears to be essential for activity if Mg2+ is to be bound at the alpha-site. The alpha- and beta-sites may be distinguished from one another by their different abilities to bind divalent-metal ions at different pH values. The occupancy of the beta-site with Zn2+ results in a decrease of protein fluorescence at pH 6. Occupancy of the alpha- and beta-sites with Co2+ results in u.v.-visible spectral changes. Spectroscopic studies with Co2+ have tentatively identified three cysteine residues at the beta-site and one at the alpha-site. Reaction with N-ethyl[14C]maleimide preferentially labels cysteine-130 at the alpha-site when Co2+ occupies the beta-site.

Quadrupolar central transition (QCT) and 13C NMR competition studies of metal ion binding to ovotransferrin

2011 ◽  
Vol 89 (7) ◽  
pp. 779-788 ◽  
Author(s):  
Jillian A. Saponja ◽  
Hans J. Vogel
Keyword(s):  
Metal Ions ◽  
Binding Sites ◽  
Metal Ion ◽  
Antimicrobial Agents ◽  
Chemical Shifts ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Ion Competition ◽  
Central Transition ◽  
C Nmr

The transferrins are a family of relatively large bilobal proteins that play a major role in the transport of Fe3+, as well as several other physiological and nonphysiological metal ions. Transferrins can also act as antimicrobial agents, by tightly sequestering iron and making it unavailable for bacterial growth. Using a combination of quadrupolar central transition (QCT) metal ion NMR (27Al, 45Sc, 51V, and 71Ga) and 13C NMR, the binding and displacement of a variety of metal ions to ovotransferrin was studied through direct metal ion competition experiments. The metal ions investigated (Al3+, Co3+, Fe3+, Ga3+, In3+, Sc3+, Y3+, and VO2+) were of differing ionic radius and charge, thus allowing for an assessment of how these factors contribute to metal ion affinity. The competition for the N- and C-terminal metal ion binding sites on ovotransferrin was directly followed by metal ion QCT NMR. Moreover, 13C NMR was used to study the two protein-bound synergistic anions (13C-labeled carbonate), whose chemical shifts are distinct and dependent on the bound metal ion that is present in the binding sites. The observed order of decreasing affinity for the metal ions studied was Fe3+ ≈ In3+ ≥ Sc3+ ≥ Ga3+ > Al3+ > VO2+ > Y3+ ≥ Co3+. These results illustrate how a combination of multinuclear solution NMR methods can provide unique insights into the ligand binding properties of larger metalloproteins.

scholarly journals Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5221
Author(s):  
Salvatore La Gatta ◽  
Linda Leone ◽  
Ornella Maglio ◽  
Maria De Fenza ◽  
Flavia Nastri ◽  
...  
Keyword(s):  
Metal Ions ◽  
Binding Site ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Structural Determinants ◽  
Binding Properties ◽  
Tetrahedral Geometry ◽  
Design Synthesis ◽  
Metal Binding Sites

Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

scholarly journals Characterization of Putative Virulence Factors of Pseudomonas aeruginosa Strain RBS Isolated from a Saltern, Tunisia: Effect of Metal Ion Cofactors on the Structure and the Activity of LasB

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
E. Rigane ◽  
R. Dutoit ◽  
S. Matthijs ◽  
N. Brandt ◽  
S. Flahaut ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Metal Ions ◽  
Virulence Factors ◽  
Binding Sites ◽  
Biofilm Formation ◽  
Metal Ion ◽  
Enzyme Stability ◽  
Inhibitory Effect ◽  
Ion Binding ◽  
Metal Ion Binding

Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium able to survive in diverse environments such as soil, plants, freshwater, and seawater. P. aeruginosa can be an opportunistic pathogen to humans when their immune system is deficient. Its pathogenicity may be linked to the production of virulence factors. We isolated P. aeruginosa strain RBS from the saltern of Sfax in Tunisia. In this study, we characterized the halotolerance, antibiotic susceptibility, and some virulence factors of strain RBS. High NaCl concentrations inhibited growth and motility. However, biofilm formation was enhanced to protect bacteria against salt stress. Among the 18 antibiotics tested, quinolones and tetracycline showed a significant inhibitory effect on growth, motility, and biofilm formation of strain RBS. β-Lactams, however, did not have any inhibitory effect on neither bacterial growth nor motility. In some cases, resistance was due, in part, to biofilm formation. We also showed that RBS produces two proteases, LasB and AprA, which have been shown to be implicated in host infection. LasB was further characterized to study the role of metal ions in enzyme stability. It possesses two distinct metal ion-binding sites coordinating a calcium and a zinc ion. The effect of metal ion chelation was evaluated as well as substitutions of residues involved in metal ion binding. Impairing metal ion binding of LasB led to a loss of activity and a sharp decrease of stability. Our findings suggest that the binding of both metal ions is interdependent as the two metal ions’ binding sites are linked via a hydrogen bond network.

De novo design of a five-stranded β-sheet anchoring a metal-ion binding site

2001 ◽  
pp. 2660-2661 ◽  
Author(s):  
Janani Venkatraman ◽  
G. A. Naganagowda ◽  
R. Sudha ◽  
Padmanabhan Balaram
Keyword(s):  
Binding Site ◽  
Metal Ion ◽  
De Novo ◽  
De Novo Design ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Β Sheet

Probing Ribosome Structure by Europium-Induced RNA Cleavage

1999 ◽  
Vol 380 (2) ◽  
pp. 243-251 ◽  
Author(s):  
S. Dorner ◽  
A. Barta
Keyword(s):  
Metal Ions ◽  
Binding Sites ◽  
Metal Ion ◽  
Divalent Metal ◽  
23S Rrna ◽  
Ion Binding ◽  
Cleavage Sites ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Binding Pockets

AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage sites, mostly those at which a general metal ion binding site had been already identified, were identical to previously described divalent metal ions. Overall, the Eu3+cleavages are most similar to the Ca2+cleavage pattern, probably due to a similar ion radius. Interestingly, several cleavage sites which were specific for Eu3+were located in regions implicated in the binding of tRNA and antibiotics. The binding of erythromycin and chloramphenicol, but not tetracycline and streptomycin, significantly reduced Eu3+cleavage efficiencies in the peptidyl transferase center. The identification of specific Eu3+binding sites near the active sites on the ribosome will allow to use the fluorescent properties of europium for probing the environment of metal ion binding pockets at the ribosome's active center.

scholarly journals The 1H nuclear-magnetic-resonance spectroscopy of cobalt(II)-β-lactamase II

1980 ◽  
Vol 187 (3) ◽  
pp. 789-795 ◽  
Author(s):  
A Galdes ◽  
H A Hill ◽  
G S Baldwin ◽  
S G Waley ◽  
E P Abraham
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Marked Change ◽  
Thiol Group ◽  
Resonance Spectroscopy ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Metal Binding Sites ◽  
1H Nuclear Magnetic Resonance ◽  
Beta Lactamase Ii

The 1H n.m.r. spectra of beta-lactamase II in the presence of Co(II) were studied. Analysis of the spectra suggests that Co(II) binds at the same two metal-binding sites as does Zn(II). The binding of Co(II) at the first site is much weaker than the binding of Zn(II) at this site, whereas the binding of Co(II) at the second site is tighter than the binding of Zn(II). The binding of Co(II) to the mono-zinc(II)-enzyme caused only one marked change in the spectrum, namely a decrease in the intensity of the resonances assigned to the C-2 and C-4 protons of one histidine residue (residue E). However, when the spectra of the apoenzyme and the Co(II)-enzyme were compared, there were many differences. A significant fraction of the protons in the whole molecule are affected by the binding of Co(II) at the first metal-ion-binding site (where the ligands are the enzyme's sole thiol group and three histidine residues). This may be because the first site is internal, or because of a difference in conformation between the apoenzyme and the mono-Co(II)-enzyme. The second site may be located on the surface of the molecule.

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