Analytical Ultracentrifugation Techniques

A non-protein organic molecule that binds to an enzyme and is essential for its activity.

An enzyme without its cofactor.

Nicotinamide adenine dinucleotide. A coenzyme that carries electrons and hydrogen ions in redox reactions.

A coenzyme derived from vitamin B1, involved in forming and breaking carbon-carbon bonds.

Vitamin B12, a coenzyme that can shuttle between different oxidation states of cobalt.

Vitamin B7, a coenzyme involved in transferring carboxyl groups.

Vitamin B6, a coenzyme that forms a Schiff base with amines and plays a role in amino acid metabolism.

Enzymes that break down proteins by cleaving peptide bonds.

A catalytic dyad is a pair of amino acids that work together to catalyze a chemical reaction. In thiol proteases, the catalytic dyad consists of a cysteine (Cys) residue and a histidine (His) residue.

The oxyanion hole is a region in the active site of an enzyme that stabilizes the negatively charged transition state of the reaction. In thiol proteases, the oxyanion hole is formed by the backbone amide nitrogen of the Cys residue and the carbonyl oxygen of the Gln residue.

Thiol proteases are a class of enzymes that use a cysteine residue as the nucleophile in the catalytic mechanism. Examples of thiol proteases include papain, ficin, and bromelain.

Aspartyl proteases are a class of enzymes that use two aspartic acid residues in their catalytic mechanism. Examples of aspartyl proteases include pepsin, chymosin, and HIV protease.

Metal ions are essential for many biological processes. Some metal ions like Na, K, Mg, and Ca are abundant in the human body and play structural roles in maintaining cell integrity and nerve impulse transmission. Other metal ions like Fe, Cu, Zn, and Mn are present in trace amounts but are essential for vital functions like oxygen transport and catalysis in redox reactions.

Proteins bind to metal ions via specific amino acids. These amino acids act as ligands, providing electrons that form coordinate bonds with the metal ion.

Porphyrins are a type of chelating ligand commonly found in biological systems. They are organic molecules with a ring structure that binds to metal ions through multiple donor atoms.

The histidine residue in a catalytic dyad is important for facilitating the reaction. It acts as a general acid/base catalyst, donating or accepting protons as needed to stabilize the transition state.

Carboxypeptidase A is a zinc-containing enzyme that catalyzes the hydrolysis of peptide bonds from the C-terminal end of proteins.

Zinc ion (Zn^2+^) in carboxypeptidase A acts as a Lewis acid, polarizing the carbonyl group (C=O) of the peptide bond, making it more susceptible to nucleophilic attack by water.

Zinc in carboxypeptidase A coordinates to water, lowering its pKa and forming a hydroxide ion (OH-), which acts as a nucleophile, attacking the carbon of the carbonyl group in the peptide bond.

Carbonic anhydrase is a zinc-containing enzyme that catalyzes the reversible hydration of carbon dioxide (CO2) to carbonic acid (H2CO3).

In carbonic anhydrase, zinc coordinates with three histidine residues and a hydroxide ion in a distorted tetrahedral geometry, providing a strong nucleophile.

Carbonic anhydrase accelerates the reaction by bringing CO2 in close proximity to the activated hydroxide ion, allowing for efficient nucleophilic attack.

Iron is the most abundant transition metal in the human body, playing crucial roles in various biological processes.

Imbalances in iron levels in the body can lead to diseases like anemia (iron deficiency) or hemochromatosis (iron overload).

A technique used to analyze the sedimentation of molecules in a centrifuge, providing information about size, shape, and interactions.

Measures the speed at which molecules sediment in a centrifuge, providing information about size, shape, and interactions.

A type of AUC that measures the distribution of molecules at equilibrium in a centrifugal field, providing information about molecular weight and interactions.

A technique that measures the binding of molecules to a surface using a change in refractive index, providing information about binding kinetics and affinity.

The bending of light as it passes from one medium to another, used in techniques like SPR to monitor binding events.

Enzymes that catalyze the addition of one oxygen atom from O2 to a substrate.

A family of heme-containing monooxygenases that are primarily found in the liver and play a role in the metabolism of various compounds.

The first main role of CYP450 enzymes is to catalyze specific oxidation steps during the biosynthesis or biodegradation of endogenous compounds, like steroids or fatty acids. This process is usually highly specific, with precise regio- and stereoselective reactions.

The second main role of CYP450 enzymes is the oxidative metabolism and elimination of exogenous compounds, like drugs, from the body. This process is generally less selective, as it aims to remove foreign substances.

A copper-based oxygen transport protein found in invertebrates, contributing to the delivery of oxygen in their circulatory systems.

Copper ions in their reduced form (Cu(I)) tend to favor bonding with softer donors like sulfur or phosphorus, often forming complexes with lower coordination numbers (2, 3, or 4).

Copper ions in their oxidized form (Cu(II)) usually prefer harder donors like oxygen or nitrogen, forming complexes with higher coordination numbers (4, 5, or 6).

Copper proteins have been categorized into three main classes, each with distinct properties and functions: Type I, Type II, and Type III.

A class of enzymes that utilize copper as a cofactor for their activity, involved in the degradation of polysaccharides.

A unique active site of LPMOs, involving coordination from the amino terminus of the protein. It's located on the enzyme's exterior.

LPMOs catalyze the oxidation of polysaccharides, specifically C-H bonds at carbon positions 1 or 4, breaking them down.

A Cu-dependent oxidase enzyme that exhibits activity on a variety of substrates, including alcohols, and catalyzes the oxidation of alcohols to aldehydes.

The reaction catalyzed by galactose oxidase involves the oxidation of alcohols to aldehydes with simultaneous reduction of oxygen.

The active site of galactose oxidase is characterized by a distorted square pyramidal geometry, with the copper atom coordinated to two histidine, two tyrosine, and one water molecule.

A modification in galactose oxidase involves the formation of a thioether linkage between a cysteine and tyrosine residues. This modification is essential for the enzyme's activity.

The thioether linkage in galactose oxidase is believed to lower the redox potential of the tyrosine residue, making it easier to oxidize to a tyrosyl radical, which is essential in the enzyme's catalytic mechanism.