Class EnzymeKinetics

java.lang.Object

org.episteme.natural.chemistry.biochemistry.EnzymeKinetics

public class EnzymeKinetics
extends Object

Enzyme kinetics calculations (Michaelis-Menten).

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Constructor Summary

Constructors

Constructor	Description
EnzymeKinetics()

Method Summary

Modifier and Type	Method	Description
static Real	catalyticEfficiency(Real kcat, Real Km)	Catalytic efficiency.
static Real	competitiveKm(Real Km, Real I, Real Ki)	Competitive inhibition: apparent Km increased.
static Real	hillEquation(Real S, Real K, Real n)	Hill equation for cooperative binding.
static Real[]	lineweaverBurkParams(Real Vmax, Real Km)	Lineweaver-Burk (double reciprocal) transformation. 1/v = (Km/Vmax) · (1/[S]) + 1/Vmax Returns array with [slope, intercept].
static Real	michaelismenten(Real S, Real Vmax, Real Km)	Michaelis-Menten equation. v = (Vmax · [S]) / (Km + [S])
static Real	noncompetitiveVmax(Real Vmax, Real I, Real Ki)	Non-competitive inhibition: Vmax decreased.
static Real	turnoverNumber(Real Vmax, Real enzymeConcentration)	Turnover number (kcat): reactions per enzyme per second. kcat = Vmax / [E]_total
static Real[]	uncompetitiveParams(Real Vmax, Real Km, Real I, Real Ki)	Uncompetitive inhibition: both Km and Vmax decreased.
static Real[]	vMaxKmFromLB(Real slope, Real intercept)	Calculates Vmax and Km from Lineweaver-Burk plot slope and intercept.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

EnzymeKinetics

public EnzymeKinetics()

Method Details

michaelismenten

public static Real michaelismenten(Real S,
 Real Vmax,
 Real Km)

Michaelis-Menten equation. v = (Vmax · [S]) / (Km + [S])

Parameters:

S - Substrate concentration

Vmax - Maximum velocity

Km - Michaelis constant

Returns:

Reaction velocity

lineweaverBurkParams

public static Real[] lineweaverBurkParams(Real Vmax,
 Real Km)

Lineweaver-Burk (double reciprocal) transformation. 1/v = (Km/Vmax) · (1/[S]) + 1/Vmax Returns array with [slope, intercept].

vMaxKmFromLB

public static Real[] vMaxKmFromLB(Real slope,
 Real intercept)

Calculates Vmax and Km from Lineweaver-Burk plot slope and intercept. Returns array with [Vmax, Km].

competitiveKm

public static Real competitiveKm(Real Km,
 Real I,
 Real Ki)

Competitive inhibition: apparent Km increased. Km_app = Km · (1 + [I]/Ki)

noncompetitiveVmax

public static Real noncompetitiveVmax(Real Vmax,
 Real I,
 Real Ki)

Non-competitive inhibition: Vmax decreased. Vmax_app = Vmax / (1 + [I]/Ki)

uncompetitiveParams

public static Real[] uncompetitiveParams(Real Vmax,
 Real Km,
 Real I,
 Real Ki)

Uncompetitive inhibition: both Km and Vmax decreased. Returns array with [Vmax_app, Km_app].

turnoverNumber

public static Real turnoverNumber(Real Vmax,
 Real enzymeConcentration)

Turnover number (kcat): reactions per enzyme per second. kcat = Vmax / [E]_total

catalyticEfficiency

public static Real catalyticEfficiency(Real kcat,
 Real Km)

Catalytic efficiency. η = kcat / Km Higher is better (diffusion limit ~10⁸-10⁹ M⁻¹s⁻¹)

hillEquation

public static Real hillEquation(Real S,
 Real K,
 Real n)

Hill equation for cooperative binding. θ = [S]^n / (K + [S]^n)

Parameters:

S - Substrate concentration

K - Apparent dissociation constant

n - Hill coefficient (n>1: positive cooperativity)

Returns:

Fractional saturation