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Biophysicochemical properties

Last modified November 28, 2014

This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.

Example: Q8W1X2

We report the following biophysical and chemical properties:

1. Absorption

The ‘Absorption’ subsection is mainly used to indicate the wavelength at which photoreactive proteins, such as fluorescent proteins, opsins, and DNA photolyases, show maximal light absorption. Additional information, such as other observed absorbance maxima (of lesser importance), lambda(max) for light emission, experimental or environmental remarks may also be included in this subsection.

Examples: O61303, P16102

2. Kinetic parameters

The ‘Kinetic parameters’ subsection is mostly used to describe kinetic data, such as Michaelis-Menten constant (KM) and maximal velocity (Vmax). Additional information (such as the substrate that shows the best catalytic efficiency, etc…) may also be included in this subsection.

For enzymes having a broad substrate specificity, we indicate KM and Vmax values for each substrate tested.

Example: Q9XZT6

The Michaelis constant (KM) is defined as the substrate concentration at which the reaction rate is half of its maximal value (or in other words it defines the substrate concentration at which half of the active sites are occupied). It indicates the affinity of an enzyme for a given substrate: the lower the KM value, the higher the affinity of the enzyme for the substrate.

Example: Q9YHY9

The maximal velocity of the reaction (or maximal rate) Vmax is the rate attained when the enzyme sites are saturated with substrate, i.e. when the substrate concentration is much higher than the KM.

Examples: Q8W1X2, Q9V2Z6

The Vmax value depends on environmental conditions, such as pH, temperature and ionic strength. This information may be added in brackets at the end of the line, when known.

Example: Q9V2Z6

If the enzyme is multifunctional or if the reaction is reversible, we annotate the Vmax for different reactions or for each direction of one reaction.

Example: P37744

3. pH dependence

The ‘pH dependence’ subsection is used to describe the optimum pH for protein activity, the variation of activity with pH variation and the pH stability of the protein.

Examples: P76316, Q58576

4. Redox potential

The ‘Redox potential’ subsection reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins.

Example: Q96JJ7

5. Temperature dependence

The ‘Temperature dependence’ subsection indicates the optimal temperature for enzyme activity and/or the variation of enzyme activity with temperature variation; the thermostability of the enzyme is also mentioned in this subsection, when known.

Example: Q38857

Note that when kinetic data were defined for a variant protein sequence, either containing a specific polymorphism or obtained by site-directed mutagenesis, they are described in the ‘Natural variant’ or ‘Mutagenesis’ subsections, respectively.

Examples: P05062, Q9S4K9

Dissociation constant (Kd) values or inhibition constant (Ki) values are not considered in this section.