Jung, Suk Hoon

Conserved Domain CombinationIn Protein Interaction

April 19, 2023

Background Conserved Domain CombinationGO term evaluation

Evaluation on Primary DC for Protein Interaction

Discussion

Contents

A set of protein domains that has been conserved through evolution

A cooperative team in order to realize the function We proposed all-confidence as an index measuring the de-

gree of conservation

We found that there are higher correlations between all-con-fidence and the functional similarity of domains than con-ventional support or confidence based approach

Conserved domain Combination

Gene Ontology term (GO term) describes the function of domains in three categories, molecular function, biological process, cellular component

GO term evaluation manifested that function of DC is more correlative with.. all-confidence than that with support Molecular function than biological process or cellular component

Conserved DC≒ Cooperative DC for molecular function

GO term Evaluation

All-confidence

supportAll-confidence

Pearson’s correlation

r = 0.205

Pearson’s correlation

r = 0.464

Inn

er

Fu

ncti

on

al S

imilar-

ity

Protein-Protein Interaction (protein binding) is a type of molecular function.

PIDC ⊂ Cooperative DC for molecular function (Conserved DC)

For the actual example using 3D structures (337 cases)

All-confidence Significancy (AS) measures the relative sig-nificance (rank) of a DC in relation to other DCs in a protein AS = 1, when the DC has highest all-confidence

Evaluation on Primary Interacting DC (PIDC)

All-conf Signifi-cancy (dci)

Evaluation on primary interacting DC

• AS distinguishes PIDCs from others• Type 1 : PIDC (269)• Type 2 : subset of PIDC (139)• Type 3 : superset of PIDC (938)• Type 4 : random DC (5252)• Type 5 : non-PIDC (803)

A

S

Further consideration 2-member DCs tends to have a higher all-conf than that of 3-

member DCs PIDCs have two domains in 297 cases among 337

In some protein, all domains participate in PIDC so has no compared DCs

Some protein has multiple PIDC according to interaction part-ner

307 proteins have PIDC in 337 cases New type

Type 1 : PIDC Type 2 : random DC Type 3 : non-PIDC

Evaluation on primary interacting DC

2-member PIDC The number of cases: 269 -> 258

# of type 1: 258 # of type 2: 237 # of type 3: 42

Evaluation 1

AS

After removal of proteins in which all domains participate in PIDC

The number of cases: 258 -> 83 # of type 1: 83 # of type 2: 237 # of type 3: 42

Evaluation 2

AS

30 Proteins use different PIDCs to interact with multiple part-ners.

In them, all PIDCs tend to have high AS, leading to confusion The number of cases: 83-> 65

# of type 1: 65 # of type 2: 170 # of type 3: 27

Evaluation 3

AS

All-confidence + GO term evaluation + evaluation on PIDC can be reported in a paper

Further considerations weaken the evaluation on Primary In-teracting DC for PPI Decrease the number of cases to be investigated Blur the functional significance of PIDC compared to other DCs

Issue