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Related Concept Videos

Coordination Compounds and Nomenclature02:54

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In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
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For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.
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The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
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Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Drugs predominantly attach to plasma proteins, with only a small percentage remaining unbound. The unbound portion can be calculated as one minus the bound fraction. Acidic drugs form large, inactive complexes by reversibly binding to plasma albumin, which prevents them from diffusing across biological barriers. These drug-protein complexes act as reservoirs for the drugs. As the concentration of unbound drugs decreases, these complexes quickly dissociate to release the free drug, maintaining...
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Pull-down of Calmodulin-binding Proteins
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Coordination to Divalent Cations by Calcium-Binding Proteins.

Masayuki Nara1, Hisayuki Morii2, Masaru Tanokura3

  • 1Department of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Chiba, Japan. nara.las@tmd.ac.jp.

Methods in Molecular Biology (Clifton, N.J.)
|February 3, 2019
PubMed
Summary

Fourier-transform infrared spectroscopy (FTIR) can study metal coordination in Ca2+-binding proteins. Deuterating proteins in D2O enables analysis of carboxylate antisymmetric stretching, overcoming spectral overlap issues in H2O.

Keywords:
Carboxylate groupCoordination structureFTIRHD exchangeSynthetic peptide analogue

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Area of Science:

  • Biophysical Chemistry
  • Spectroscopy
  • Protein Science

Background:

  • Fourier-transform infrared spectroscopy (FTIR) is vital for analyzing metal coordination in carboxylate groups (COO-) of glutamate (Glu) and aspartate (Asp) within Ca2+-binding proteins.
  • The symmetric stretch of COO- is observable in H2O, but the antisymmetric stretch is obscured by the amide II band.

Purpose of the Study:

  • To develop a reliable method for analyzing the carboxylate antisymmetric stretch in Ca2+-binding proteins using FTIR.
  • To overcome spectral interferences in aqueous solutions.

Main Methods:

  • Utilizing Fourier-transform infrared spectroscopy (FTIR) to analyze protein samples.
  • Employing H2O for studying the symmetric stretch of carboxylate groups.
  • Implementing complete deuteration of exchangeable protons by incubating apoprotein in D2O with mild heating to isolate the antisymmetric stretch.

Main Results:

  • Successfully obtained reliable infrared spectra in the carboxylate antisymmetric stretch region.
  • Demonstrated the effectiveness of D2O exchange for spectral resolution.

Conclusions:

  • Complete deuteration of proteins in D2O is a crucial method for accurately studying the carboxylate antisymmetric stretch via FTIR.
  • This technique enhances the understanding of metal-ligand interactions in Ca2+-binding proteins.