-
Current Opinion in Chemical Biology Apr 2002Freeze-trapping reaction intermediates in macromolecular crystals is now a proven technique for obtaining their high-resolution structures by X-ray crystallography. The... (Review)
Review
Freeze-trapping reaction intermediates in macromolecular crystals is now a proven technique for obtaining their high-resolution structures by X-ray crystallography. The structural study of metalloprotein mechanisms has spearheaded this work, mainly because of the increased availability of single-crystal UV/visible spectrophotometry that enables reaction monitoring in the crystalline state. In particular, through formation of the frozen glass state, the stabilization of intermediates involving dissolved gases has yielded some of the most spectacular results. Metalloprotein systems still dominate this field, and the most recent successes, along with the accompanying advances in methodology, are presented.
Topics: Cold Temperature; Crystallization; Crystallography, X-Ray; Cytochromes; DNA Polymerase beta; Electron Transport Complex IV; Ligands; Metalloproteins; Nitrite Reductases
PubMed: 12039005
DOI: 10.1016/s1367-5931(02)00300-9 -
Science (New York, N.Y.) Jun 2017The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and...
The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.
Topics: Animals; Cytochromes c; Horses; Ligands; Metalloproteins; Metals; Protein Stability; Spectrometry, X-Ray Emission
PubMed: 28642436
DOI: 10.1126/science.aam6203 -
Metallomics : Integrated Biometal... Apr 2021Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular...
Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.
Topics: Binding Sites; Biological Evolution; Humans; Metalloproteins; Phylogeny; Porphobilinogen Synthase; Protein Conformation; Quantum Theory; Zinc
PubMed: 33791795
DOI: 10.1093/mtomcs/mfab017 -
Metallomics : Integrated Biometal... Jan 2019
Topics: Animals; Computational Biology; Humans; Metalloproteins; Metals; Research Personnel
PubMed: 30632595
DOI: 10.1039/c8mt90047g -
Metallomics : Integrated Biometal... Jan 2018Nucleic acid enzymes (NAEs) are catalytically active RNA and DNA molecules. NAEs with RNA-cleaving activity are most extensively studied for applications in analytical... (Review)
Review
Nucleic acid enzymes (NAEs) are catalytically active RNA and DNA molecules. NAEs with RNA-cleaving activity are most extensively studied for applications in analytical chemistry, gene therapy and nanotechnology. Most NAEs require metal ions for activity. From a biochemical standpoint, these NAEs are reminiscent of metalloprotein enzymes with metal binding sites. While most NAEs require a single metal for the reaction, more and more recent examples have emerged that use two or even three metals for the reaction. The metal binding profile is sharper for these NAEs if they use the same metal ion due to cooperativity. Detailed studies have indicated examples of lanthanide and Ca binding DNAzymes, where the metals interact with the non-bridging oxygen atoms in the scissile phosphate, and these DNAzymes often have a very strong thio effect that cannot be rescued by adding thiophilic metals. Another type uses multiple different metals, where one metal interacts with the scissile phosphate and the other binds to the catalytic loop for allosteric interactions. Such allosteric NAEs can also be obtained via rational design or intentional selection based on existing NAEs. These multi-metal NAEs might be useful as logic gates with metal ions as inputs. In this article, we review different types of NAEs based on their use of metal ions. The NAEs reviewed include ribozymes, DNAzymes and rationally designed aptazymes. Finally, their emerging applications are discussed, and some future research opportunities are proposed.
Topics: Animals; DNA, Catalytic; Humans; Metalloproteins; Metals
PubMed: 29094140
DOI: 10.1039/c7mt00268h -
Proceedings of the National Academy of... Mar 2003The sense of smell is arguably our most primal faculty and also the least understood. Even our own olfactorily impaired species is capable of detecting approximately...
The sense of smell is arguably our most primal faculty and also the least understood. Even our own olfactorily impaired species is capable of detecting approximately 10,000 distinct scents [Buck, L. & Axel, R. (1991) Cell 65, 175-187]. To achieve that amazing diversity, mammals have approximately 1,000 olfactory genes, which accounts for approximately 3% of their entire genome [Mombaerts, P. (1999) Science 286, 707-711]. The olfactory receptors (ORs) are believed to be seven-helix transmembrane proteins, with an odorant-binding site on the periplasmic domain and a G protein-binding site on the cytoplasmic domain. Odorants first bind to an OR, which then undergoes some structural change that triggers the G protein activation and the following cascade of events leading to nerve cell activity. The structural details of ORs, however, remain to be determined. In this paper, we will describe a hypothesis in which metal ions play an important role for odorant recognition. We analyze the predicted structure and consensus sequence of the ORs and propose a metal-binding site in the loop between fourth and fifth helix (4-5 loop). We have prepared synthetically a pentapeptide that contains this putative binding site and find that it not only has high affinity for binding Cu(II) and Zn(II) ions, but that it also undergoes a dramatic transition to an alpha-helical structure upon metal ion binding. Based on these observations, we propose a "shuttlecock" mechanism for the possible structural change in ORs upon odorant binding. This mechanism involves membrane penetration of the 4-5 loop after residue charge neutralization by metal ion binding.
Topics: Amino Acid Sequence; Binding Sites; Circular Dichroism; Humans; Markov Chains; Metalloproteins; Models, Biological; Models, Molecular; Molecular Sequence Data; Molecular Structure; Odorants; Protein Structure, Secondary; Receptors, Odorant
PubMed: 12610211
DOI: 10.1073/pnas.262792899 -
Molecules (Basel, Switzerland) Jan 2021In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and... (Review)
Review
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
Topics: Ionic Liquids; Metalloproteins; Structure-Activity Relationship
PubMed: 33478102
DOI: 10.3390/molecules26020514 -
The FEBS Journal Jul 2010
Topics: Animals; Brain Diseases; Coordination Complexes; Humans; Metalloproteins; Metallothionein 3; Nerve Tissue Proteins; Structure-Activity Relationship
PubMed: 20561056
DOI: 10.1111/j.1742-4658.2010.07715.x -
Proceedings of the National Academy of... Dec 2016Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating...
Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)] complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is ∼1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.
Topics: Amino Acids; Cloning, Molecular; Computational Biology; Computer Simulation; Crystallography, X-Ray; Metalloproteins; Metals; Models, Molecular; Protein Conformation; Protein Engineering; Protein Interaction Mapping; Protein Multimerization; Pyridines; Software
PubMed: 27940918
DOI: 10.1073/pnas.1600188113 -
ACS Applied Materials & Interfaces Jan 2020To develop biomaterials that easily and reversibly remove trace amounts of metal ions, we synthesized PNIPAM--CadRP, a thermally sensitive hybrid hydrogel by...
To develop biomaterials that easily and reversibly remove trace amounts of metal ions, we synthesized PNIPAM--CadRP, a thermally sensitive hybrid hydrogel by immobilizing a reconstituted cadmium binding peptide (CadRP) derived from the metalloregulatory protein CadR in a poly(-isopropylacrylamide) (PNIPAM) gel network. The hybrid hydrogel retains the properties of the immobilized peptide and highly sensitively and selectively binds Cd(II) ions. The thermally sensitive properties of the hybrid hydrogel, which swells at low temperatures (<34 °C) and shrinks at high temperatures, provides a driving force sufficient to alternate the conformation of the immobilized CadRP such that the peptide captures and releases metal ions at high and low temperatures, respectively. Using this novel hybrid gel, we captured nanomolar Cd(II) from samples of environmental water in a highly efficient manner, leading to a practical and repeatedly reusable material to remediate our environment.
Topics: Acrylic Resins; Cadmium; Hydrogels; Metalloproteins; Peptides; Temperature; Water Pollutants, Chemical
PubMed: 31860264
DOI: 10.1021/acsami.9b19306