Comparing Nonbonded Metal Ion Models in the Divalent Cation Binding Protein PsaA
Hugo MacDermott-Opeskin1, Christopher A McDevitt2, Megan L O'Mara1
1Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia.
Journal of Chemical Theory and Computation
|February 15, 2020
Summary
Choosing the right ion model is crucial for accurately simulating metal binding proteins. The 12-6-4 ion model best captures the dynamics of manganese and zinc binding in PsaA, a protein from Streptococcus pneumoniae.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Divalent metal cations are vital for biological functions.
- Accurate molecular dynamics (MD) force fields for divalent metal ions remain a challenge.
- Protein metal binding dynamics are sensitive to ion modeling.
Purpose of the Study:
- To investigate the impact of different ion models on the dynamics of PsaA, a metal binding protein.
- To compare the performance of 12-6, 12-6-4, and multisite ion models.
- To provide a framework for rationalizing experimental metal binding data.
Main Methods:
- Extensive unbiased molecular dynamics simulations.
- Free energy calculations for ion binding and release.
- Comparison of three nonbonded ion models (12-6, 12-6-4, multisite).
Main Results:
- Ion model choice significantly influences observed coordination geometries and metal binding dynamics in PsaA.
- The 12-6-4 ion model showed the most accurate representation of Mn2+ binding.
- Simulations with the 12-6-4 model yielded a conformational ensemble for Mn-bound PsaA similar to the open crystallographic state.
Conclusions:
- The 12-6-4 ion model is recommended for future simulations of divalent cation binding proteins.
- Accurate ion modeling is essential for understanding protein-metal interactions.
- This study refines the model of PsaA metal binding and offers insights into divalent metal cation dynamics.
More Related Videos
07:54Analysis of AtHIRD11 Intrinsic Disorder and Binding Towards Metal Ions by Capillary Gel Electrophoresis and Affinity Capillary Electrophoresis
Published on: August 22, 2018
6.3K
14:44Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
10.0K
Related Concept Videos
02:42Valence Bond Theory
10.9K
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
10.9K
02:46Crystal Field Theory - Tetrahedral and Square Planar Complexes
47.6K
Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
47.6K
02:58Crystal Field Theory - Octahedral Complexes
30.1K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
30.1K
01:22EDTA: Chemistry and Properties
3.1K
Polydentate ligands are most widely used in complexometric titrations because they form more stable complexes with the metal ions than mono- or bidentate ligands due to the chelate effect. Examples of polydentate ligands are ethylenediaminetetraacetic acid (EDTA), crown ethers, and cryptands. The most important feature of optimal polydentate ligands is the ability to form 1:1 complexes in a single-step process. Amino carboxylic acid derivatives are frequently used as complexing agents. EDTA is...
3.1K
02:51Metal-Ligand Bonds
23.5K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
23.5K
01:49Conserved Binding Sites
5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K