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Metallomics : Integrated Biometal... Jan 2013
Topics: Animals; Humans; Metalloproteins; Metals; Periodicals as Topic; Proteomics
PubMed: 23238130
DOI: 10.1039/c2mt90067j -
Journal of Molecular Graphics &... Jun 2024Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin...
Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin unfolding on the atomic scale. Different simulation techniques were applied, and due to the dissociation of covalent/hydrogen bonds, this protein demonstrates several intermediate states in force-extension behavior. A conceptual model based on the cohesive finite element method was developed to consider the intermediate damages that occur during unfolding. This model is based on force-displacement curves derived from molecular dynamics results. The proposed conceptual model is designed to accurately identify bond rupture points and determine the associated forces. This is achieved by conducting a thorough comparison between molecular dynamics and cohesive finite element results. The utilization of a viscoelastic cohesive zone model allows for the consideration of loading rate effects. This rate-dependent model can be further developed and integrated into the multiscale modeling of large assemblies of metalloproteins, providing a comprehensive understanding of mechanical behavior while maintaining a reduced computational cost.
Topics: Rubredoxins; Metalloproteins; Molecular Dynamics Simulation; Mechanical Phenomena; Hydrogen Bonding
PubMed: 38442439
DOI: 10.1016/j.jmgm.2024.108749 -
Analytical Biochemistry May 1990The feasibility of using directly coupled size exclusion high-performance liquid chromatography inductively coupled plasma mass spectroscopy (HPLC/ICP-MS) for the...
The feasibility of using directly coupled size exclusion high-performance liquid chromatography inductively coupled plasma mass spectroscopy (HPLC/ICP-MS) for the separation and subsequent elemental analysis of metalloproteins in biological samples has been studied. Data, on up to eight elements, was acquired simultaneously and the reconstructed elemental profiles from the chromatographed samples were quantified by flow injection analysis. Absolute and relative detection limits, reproducibility, operational dynamic range, and linearity of response were initially evaluated by analyzing standards of metallothionein protein of known elemental composition for Cd, Zn, and Cu. There was evidence of displacement of Zn from the protein during chromatography and the substitution of Cu sequestered from the mobile phase. Cd associated with the protein was fully recovered during chromatography. Memory effects, due to protein adsorption to the glassware in the torch box, were minimal and there was no degradation of the resolution of the chromatographed peak during extended transport through the HPLC/ICP-MS interface. The versatility of the technique has been demonstrated by the quantitative multi-element analysis of cytosolic metal-binding proteins separated from the polychaete worm Neanthes arenaceodentata. Fidelity of analysis has been demonstrated by two independent procedures: first, by comparing the elemental profiles obtained by directly aspirating the HPLC eluant into the ICP-MS to those obtained by collecting fractions and quantifying the metal content of the proteins in the conventional analytical mode; second, by comparing the stable isotopic profiles for 114Cd obtained by simultaneous ICP-MS analysis with radiometric profiles of 109Cd obtained by counting radioactivity associated with collected fractions.(ABSTRACT TRUNCATED AT 250 WORDS)
Topics: Animals; Cadmium; Chromatography, High Pressure Liquid; Copper; Cytosol; Mass Spectrometry; Metalloproteins; Polychaeta; Zinc
PubMed: 2363489
DOI: 10.1016/0003-2697(90)90066-i -
Bioconjugate Chemistry 1992Cytochrome c (cyt) and zinc cytochrome c (Zncyt) are separately cross-linked to plastocyanin (pc) by the carbodiimide EDC according to a published method. The changes in... (Comparative Study)
Comparative Study
Metalloprotein complexes for the study of electron-transfer reactions. Characterization of diprotein complexes obtained by covalent cross-linking of cytochrome c and plastocyanin with a carbodiimide.
Cytochrome c (cyt) and zinc cytochrome c (Zncyt) are separately cross-linked to plastocyanin (pc) by the carbodiimide EDC according to a published method. The changes in the protein reduction potentials indicate the presence of approximately two amide cross-links. Chromatography of the diprotein complexes cyt/pc and Zncyt/pc on CM-52 resin yields multiple fractions, whose numbers depend on the eluent. UV-vis, EPR, CD, MCD, resonance Raman, and surface-enhanced resonance Raman spectra show that cross-linking does not significantly perturb the heme and blue copper active sites. Degrees of heme exposure show that plastocyanin covers most of the accessible heme edge in cytochrome c. Impossibility of cross-linking cytochrome c to a plastocyanin derivative whose acidic patch had been blocked by chemical modification shows that it is the acidic patch that abuts the heme edge in the covalent complex. The chromatographic fractions of the covalent diprotein complex are structurally similar to one another and to the electrostatic diprotein complex. Isoelectric points show that the fractions differ from one another in the number and distribution of N-acylurea groups, byproducts of the reaction with the carbodiimide. Cytochrome c and plastocyanin are also tethered to each other via lysine residues by N-hydroxysuccinimide diesters. Tethers, unlike direct amide bonds, allow mobility of the cross-linked molecules. Laser-flash-photolysis experiments show that, nonetheless, the intracomplex electron-transfer reaction cyt(II)/pc(II)----cyt(III)/pc(I) is undetectable in complexes of either type. Only the electrostatic diprotein complex, in which protein rearrangement from the docking configuration to the reactive configuration is unrestricted, undergoes this intracomplex reaction at a measurable rate.
Topics: Amides; Chromatography, Ion Exchange; Cross-Linking Reagents; Cytochrome c Group; Electron Spin Resonance Spectroscopy; Electrons; Ethyldimethylaminopropyl Carbodiimide; Kinetics; Metalloproteins; Oxidation-Reduction; Plastocyanin; Zinc
PubMed: 1329988
DOI: 10.1021/bc00017a005 -
Nature Aug 2009Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how... (Review)
Review
Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.
Topics: Biotechnology; Drug Design; Enzymes; Metalloproteins; Protein Conformation; Protein Engineering; Substrate Specificity
PubMed: 19675646
DOI: 10.1038/nature08304 -
Journal of Chemical Theory and... Aug 2019Many biological processes are based on molecular recognition between highly charged molecules such as nucleic acids, inorganic ions, charged amino acids, etc. For such...
Many biological processes are based on molecular recognition between highly charged molecules such as nucleic acids, inorganic ions, charged amino acids, etc. For such cases, it has been demonstrated that molecular simulations with fixed partial charges often fail to achieve experimental accuracy. Although incorporation of more advanced electrostatic models (such as multipoles, mutual polarization, etc.) can significantly improve simulation accuracy, it increases computational expense by a factor of 5-20×. Indirect free energy (IFE) methods can mitigate this cost by modeling intermediate states at fixed-charge resolution. For example, an efficient "reference" model such as a pairwise Amber, CHARMM, or OPLS-AA force field can be used to derive an initial estimate, followed by thermodynamic corrections to a more advanced "target" potential such as the polarizable AMOEBA model. Unfortunately, all currently described IFE methods encounter difficulties reweighting more than ∼50 atoms between resolutions due to extensive scaling of both the magnitude of the thermodynamic corrections and their statistical uncertainty. We present an approach called "simultaneous bookending" (SB) that is fundamentally different from existing IFE methods based on a tunable sampling approximation, which permits scaling to thousands of atoms. SB is demonstrated on the relative binding affinity of Mg/Ca to a set of metalloproteins with up to 2972 atoms, finding no statistically significant difference between direct AMOEBA results and those from correcting Amber to AMOEBA. The ability to change the resolution of thousands of atoms during reweighting suggests the approach may be applicable in the future to protein-protein binding affinities or nucleic acid thermodynamics.
Topics: Animals; Calcium; Cations, Divalent; Databases, Protein; Humans; Magnesium; Metalloproteins; Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; Software; Static Electricity; Thermodynamics
PubMed: 31268700
DOI: 10.1021/acs.jctc.9b00147 -
Journal of Inorganic Biochemistry Sep 2024CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite... (Review)
Review
CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite its merits, traditional homogeneous catalysis, often faces challenges in efficiency, selectivity, and sustainability towards this transformation. In this context, artificial metalloenzymes (ArMs), resulting from the incorporation of a catalytically-competent metal cofactor within an evolvable protein scaffold, bridges the gap between the efficiency of enzymatic transformations and the versatility of transition metal catalysis. Accordingly, ArMs have emerged as attractive tools for various challenging catalytic transformations. Additionally, the coming of age of directed evolution has unlocked unprecedented avenues for optimizing enzymatic catalysis. Taking advantage of their genetically-encoded protein scaffold, ArMs have been evolved to catalyze various CH functionalization reactions. This review delves into the recent developments of ArM-catalyzed CH functionalization reactions, highlighting the benefits of engineering the second coordination sphere around a metal cofactor within a host protein.
Topics: Metalloproteins; Catalysis; Protein Engineering; Hydrogen
PubMed: 38852295
DOI: 10.1016/j.jinorgbio.2024.112621 -
Current Opinion in Chemical Biology Apr 2001Judicious control of ligand steric bulk and auxiliary structural elements enables the construction of novel synthetic complexes that model the properties of... (Review)
Review
Judicious control of ligand steric bulk and auxiliary structural elements enables the construction of novel synthetic complexes that model the properties of metalloprotein active sites, thus providing insight into their structure and function. Major recent developments include the synthesis of a number of unusual and biologically relevant complexes of copper and iron using elaborate N-donor and O-donor ligands.
Topics: Benzoates; Binding Sites; Copper; Electron Transport Complex IV; Iron; Ligands; Metalloproteins; Models, Chemical; Molecular Conformation
PubMed: 11282346
DOI: 10.1016/s1367-5931(00)00189-7 -
Journal of Biological Inorganic... Jun 2019Metal coordination with proteinaceous ligands has greatly expanded the chemical toolbox of proteins and their biological roles. The structure and function of natural... (Review)
Review
Metal coordination with proteinaceous ligands has greatly expanded the chemical toolbox of proteins and their biological roles. The structure and function of natural metalloproteins have been determined according to the physicochemical properties of metal ions bound to the active sites. Concurrently, amino acid sequences are optimized for metal coordination geometry and/or dedicated action of metal ions in proteinaceous environments. In some occasions, however, natural enzymes exhibit promiscuous reactivity with more than one designated metal ion, under in vitro and/or in vivo conditions. In this review, we discuss selected examples of metalloenzymes that bind various first-row, mid- to late-transition metal ions for their native catalytic activities. From these examples, we suggest that environmental, inorganic, and biochemical factors, such as bioavailability, native organism, cellular compartment, reaction mechanism, binding affinity, protein sequence, and structure, might be responsible for determining metal selectivity or promiscuity. The current work proposes how natural metalloproteins might have emerged and adapted for specific metal incorporation under the given circumstances and may provide insights into the design and engineering of de novo metalloproteins.
Topics: Amino Acid Sequence; Enzymes; Metalloproteins; Metals; Substrate Specificity
PubMed: 31115763
DOI: 10.1007/s00775-019-01667-0 -
Current Opinion in Biotechnology Aug 1991A dramatic increase in the number of solved metalloprotein structures and recent breakthroughs in structural analysis have provided a sufficiently detailed understanding... (Review)
Review
A dramatic increase in the number of solved metalloprotein structures and recent breakthroughs in structural analysis have provided a sufficiently detailed understanding of the structural chemistry of some metal-binding sites to allow successful design. As a result, metal-binding site design is now one of the most powerful and promising approaches for influencing protein folding, assembly, stability and catalysis.
Topics: Amino Acid Sequence; Binding Sites; Metalloproteins; Metals; Models, Molecular; Molecular Sequence Data; Protein Engineering
PubMed: 1367679
DOI: 10.1016/0958-1669(91)90084-i