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Globular Protein Functions and Ligand Binding, Study notes of Biochemistry

Massachusetts College of Pharmacy & Health Sciences (MCPHS)Biochemistry

An overview of globular protein functions, focusing on the reversible binding of ligands, transport of molecules, defense against pathogens, muscle contraction, and biological catalysis. It explains the basics of protein-ligand binding interactions, including the concepts of reversible equilibrium, ligands, and binding sites. The document also discusses the specificity of protein binding, including the lock-and-key model and induced fit, and provides a quantitative description of ligand binding using association and dissociation rates. It also includes graphical analysis of bound fraction.

Typology: Study notes

2022/2023

Available from 05/23/2025

asia-adams-lemar
asia-adams-lemar 🇺🇸

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bg1
Globular
Protein
Functions
Functions
/
Examples
keys
to
Function
I.
Storage
of
tons
/
molecules
1.
Reversible
binding
of
ligands
↳
myoglobin
,
ferritin
2.
Specific
ligands
/
binding
sites
2.
Transport
10ns
/
molecules
↳
hemoglobin
,
serotonin
transporter
3.
Induced
fit
-
Ligand
binding
(
conformational
/
dramatic
changes
)
3.
Defense
against
pathogens
↳
antibodies
,
cytokines
4.
Cooperatively
-
Multi
subunit
proteins
(
conformational
changes
in
4.
Muscle
contraction
one
subunit
that
affects
others
)
↳
actin
,
myosin
5.
Regulated
interactions
5.
Biological
catalysts
↳
chymotrypsin
,
lysozyme
protein
-
Ligand
Binding
Interaction
Basics
Reversible
◦
transient
process
of
equilibrium
Ty
]
'¥¥I÷
󲰛
↳
a-
+
B
AB
←
{§EA@⑥{Ñf
r
Ligands
→
Molecule
that
binds
+
◦
proteins
:÷i󲰜:¥É¥¥É*ÉsÉÉ󲰜
g
-
%↑ÉÉÉ¥•&%
↳
typically
small
'
2
Binding
site
→
Region
in
protein
that
binds
ligands
non
covalent
bonds
Ligand
binds
-10
same
Non
covalent
interactions
dictating
protein
structure
,
,g§
↳
transient
E󲰜⇐??Ñ¥EÉEHÉ•ñ
BaÉ
"
Site
'
Examples
Of
Binding
Strength
typc.at#-r-gandnterac-10nsse9uence-spec-fpr-ein-DNA
Specificity
:
Lock
-
and
-
Key
Model
Biotin
-
avidin
proteins
→
high
specificity
AÉn
É
↓
↳
explained
by
complementary
of
the
binding
site
/
ligand
io-FY-TY-TTL-TY-o-%Ff.TT
-2
Complementary
in
:
↳
Size
,
Shape
,
Charge
,
hydrophobic
/
hydrophilic
high
affinity
Kd
(
M
)
low
affinity
Lock
and
key
model
by
Emil
Fisher
(
1894
)
→
complementary
surfaces
are
performed
Specificity
:
Induced
Fit
Conformational
Changes
→
ligand
binding
l
Daniel
Koshlan d
1958
)
↳
Induced
fit
;
tighter
binding
/
variable
affinity
of
different
ligands
⑧]
y
⑧f
󲰛
Y⑧(
Ligand
and
protein
change
conformations
R+Em
󲰛
FINE
pf2

Partial preview of the text

Download Globular Protein Functions and Ligand Binding and more Study notes Biochemistry in PDF only on Docsity!

Globular

Protein

Functions

Functions

Examples

keys

to Function

I.

Storage

of tons /

molecules

  1. Reversible

binding

of

ligands

myoglobin ,

ferritin

Specific ligands

/ binding

sites

Transport 10ns /

molecules

hemoglobin ,

serotonin transporter

Induced fit

Ligand binding

(conformational /

dramatic

changes

)

  1. Defense

against

pathogens

antibodies , cytokines

Cooperatively

Multisubunit proteins

(

conformational

changes

in

Muscle contraction one subunit that affects others )

actin , myosin

Regulated

interactions

Biological

catalysts

chymotrypsin

, lysozyme

protein

Ligand

Binding

Interaction

Basics

Reversible

◦

transient

process

of equilibrium

Ty

]

'¥¥I÷

a-+ B

AB ←

{§EA@⑥{Ñf

r

Ligands

→ Molecule that binds +◦ proteins

:÷i :¥É¥¥É*ÉsÉÉ g

%↑ÉÉÉ¥•&%

typically

small

'

Binding

site → Region

in protein

that binds

ligands

noncovalent bonds

Ligand

binds -10 same Non covalent interactions

dictating protein

structure

, ,g§

transient

E ??Ñ¥EÉEHÉ•ñ

BaÉ

"

Site

Examples

Of

Binding

Strength

typc.at#-r-gandnterac-10nsse9uence-spec-fpr-ein-DNA

Specificity

: Lock

and

Key

Model

Biotin

  • avidin

proteins

→

high specificity

↓ AÉn É explained by complementary

of the

binding

site / ligand

io-FY-TY-TTL-TY-o-%Ff.TT

Complementary

in

:

Size ,

Shape , Charge , hydrophobic

/hydrophilic

high

affinity

Kd (M )

low affinity

Lock

and

key

model by

Emil Fisher (

1894 ) →

complementary

surfaces

are performed

Specificity

: Induced
Fit

Conformational Changes

→

ligand binding

lDaniel Koshland

1958 )

Induced fit

; tighter

binding /

variable affinity

of different ligands

⑧]

y ⑧f

Y⑧(

Ligand

and protein change

conformations

R+Em FINE

Binding

:

Quantitative

Description

ligand

CL)

binds reversibly

to a site in Protein

( P)

Described

quantitatively

by

the

association rate

ka

CHEEK

.

(☒÷÷÷÷

:

""""

Kd

Process will

reach equilibrium ;

association /

dissociation

P L PL

ka [P ]

.CL

]

=

Kd [

PL]

Equilibrium

constant → equilibrium

association constant ka

or the equilibrium

constant

,

Kd

Binding

:

Analysis

in Terms

of the Bound Fraction

Fraction of occupied binding

sites

( ⊖ ) Ka

= [P =

g

ka =

CPL]

[P]

.

[L]

¥5s

Substituting

[PL ] with Ka [L]

[P]

;

eliminate [PL]

Eliminating

[P ] /

rearranging

causes equilibrium

association constant

⊖

=

[

PL]

equilibrium dissociation

constant

[PL]

[P]

Binding

:

Graphical Analysis

Fraction of bound sites depends

on free

ligand

concentration and ka

Experimentally

: ⊖

_

I

]

⊖

=

Ka

[

L

]

[

P

]

[L ]+Ñd

ligand

concentration known

[L] ≈ [

+◦+a,

[P]_

Kd

→ determined

graphically

/ least-squares regression

⑤

=

[

L

]

[

L a

✗ ◦

;

it

'

[

L

]

i

G- =

I [

L

]

Ka

◦

ka→→

[

L

]

arbitrary

units )