Protein regulation: non-covalent changes

Non-covalent protein regulation

Control of protein activity through reversible binding interactions without chemical modification

Effect of binding

Can block active site or induce conformational changes affecting activity

Reversible regulation

Allows repeated switching on/off, common in signalling pathways

Regulation outcomes

Can affect activity, localisation, and specificity

Inhibition mechanism

Usually involves direct blockage of catalytic site

Activation mechanism

Often involves binding followed by conformational change

α1-antitrypsin

Protein inhibitor of neutrophil elastase produced in the liver

Elastase function

Breaks down proteins during immune defence

Elastase overactivity

Causes damage to lung tissue

Smoking effect

Oxidises methionine in α1-antitrypsin, reducing inhibition

Emphysema cause

Excess elastase activity due to inactive inhibitor

Trypsin inhibitors

Proteins that block trypsin activity via substrate mimicry

S1 pocket interaction

Lysine residues of inhibitor bind to aspartate in enzyme active site

Polymerisation inhibition

Formation of protein filaments reduces enzyme activity

Acs1 regulation

Filament formation prevents active conformation

Dormancy regulation

Filaments form in dormant cells and depolymerise during activation

Substrate mimicry

Inhibitor resembles substrate and binds to active site

CagA protein

H. pylori protein mimicking kinase substrates to inhibit activity

Subcellular localisation regulation

Control of protein activity by changing its location in the cell

AKAP proteins

Anchor protein kinase A to specific cellular locations

E1A viral protein

Mimics AKAP to redirect PKA to nucleus

Viral replication regulation

Mislocalised PKA enhances viral gene expression

Ras protein

GTPase involved in signal transduction

Ras active state

Bound to GTP and transmits signal

Ras inactive state

Bound to GDP and does not signal

GTPase activating protein (GAP)

Regulates Ras by accelerating GTP hydrolysis

GAP mechanism

Contributes residue to catalytic site to speed reaction

Ras activation cycle

GDP exchanged for GTP to activate, hydrolysis returns to inactive state

Ras mutation consequence

Disrupted regulation can lead to cancer

Regulation of specificity

Protein function altered by association with different regulatory subunits

Phosphatase specificity

Determined by associated regulatory proteins

Feedback inhibition

End product of pathway inhibits earlier step

Purpose of feedback inhibition

Prevents overproduction of metabolites

First enzyme inhibition

Common target of pathway end-product inhibition

Aspartate transcarbamoylase (ATCase)

Enzyme in pyrimidine synthesis pathway

CTP inhibition

Binds allosteric regulatory subunits of ATCase

Allosteric inhibition effect

Conformational change reduces catalytic activity

cAMP

Second messenger in signalling pathways

Protein kinase A (PKA)

Activated by binding of cAMP

PKA regulatory subunit

Contains region that mimics substrate and blocks active site

Calcium regulation

Intracellular Ca²⁺ levels control protein activity

Calmodulin

Calcium-binding protein that changes conformation upon binding Ca²⁺

Myosin light chain kinase

Activated by Ca²⁺-calmodulin complex

Muscle contraction regulation

Triggered by phosphorylation of myosin light chain

Ion regulation

Binding of small ions can alter protein structure and function

Diphtheria toxin repressor

Regulated by Fe²⁺ binding

Iron effect

Alters protein conformation to enable DNA binding

pH regulation

Protein activity controlled by environmental acidity

Endosomes

Acidic compartments in eukaryotic cells

Cathepsin D

Protease active in acidic endosomes

Neutral pH effect

N-terminal region blocks active site

Acidic pH effect

Conformational change allows substrate access

Combined regulation

Proteins often controlled by multiple mechanisms

Pepsinogen activation

Requires acidic pH and proteolytic cleavage

Dual regulation purpose

Prevents premature activation

Glycogen phosphorylase regulation

Controlled by both allosteric effectors and phosphorylation

Energy charge regulation

Activity depends on AMP/ATP ratio

AMP effect

Promotes active form

ATP effect

Promotes inactive form

Molecular regulation principle

Protein activity controlled by altering interactions with substrates or partners

Protein regulation importance

Enables rapid responses in metabolism and signalling

Non-covalent regulation advantage

Faster than gene expression changes and reversible