Chapter 5

Protein Function
 Outlines

I. Introduction to Protein
II. Reversible Binding of a Protein to a Ligand: Oxygen-
Binding Proteins
III. Complementary Interactions Between Proteins and
Ligands: The Immune System and Immunoglobulins
IV. Protein Interaction Modulated by Chemical Energy: Actin,
Myosin, and Molecular Motors

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 I. Introduction to proteins
Proteins are made up of many different amino acids linked together. There are twenty different of
these amino acid building blocks commonly found in plants and animals. A typical protein is made up
of 300 or more amino acids and the specific number and sequence of amino acids are unique to each
protein.

Actin monomer (G-actin) is a water-soluble

Muscle Contraction and a Really Cool Protein Called Myosin globular structural protein with a molecular weight
of 42 kDa, consisting of 375 or 374 amino acid
residues.
 I. Introduction to proteins
 Proteins are dynamic molecules whose functions almost invariably depend on interactions
with other molecules.
 The functions of many proteins involve the reversible binding of other molecules. A molecule
bound reversibly by a protein is called a ligand. A ligand may be any kind of molecule,
including another protein.
Iron Fe 2+

Ligands include substrates, inhibitors, activators,

signaling lipids, and neurotransmitters.
II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins

Reversible Binding of a Protein to a Ligand

Proteins are flexible. Changes in conformation may be subtle, reflecting molecular

vibrations and small movements of amino acid residues throughout the protein.
The binding of a protein and ligand is often coupled to a conformational change in the protein that
makes the binding site more complementary to the ligand, permitting tighter binding.

The classic ligands that reversibly bind to hemoglobin, dioxygen, carbon dioxide, and protons, are
bound covalently. Dioxygen binds to a heme Fe2+, protons obviously bind to proton acceptors
(like His), while CO2 binds covalently as if forms a carbamate with the N terminus of one of the
hemoglobin chains.
II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins
The protein found in the red blood cells responsible for transporting oxygen molecules is hemoglobin. It
is also a type of metalloprotein because of the presence of metallic iron in its structure. The molecule of
hemoglobin is also responsible for transporting the carbon dioxide molecules in the blood.

Hemoglobin Contains a non-protein group and protein group.

Heme group is the non-protein Protein part contains the

group of iron atoms globular protein
 II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins
 Oxygen is poorly soluble in aqueous solutions and cannot be carried to tissues in sufficient
quantity if it is simply dissolved in blood serum

Heme group consists of a complex organic ring structure, protoporphyrin, to which is bound a single iron atom
in its ferrous (Fe2+).
II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins
Protein part contains the globular protein

Most globular proteins are water-soluble. These proteins have amino acids that are hydrophilic
on the surface, allowing them to interact with water molecules.
II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins
 II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins

Myoglobin Has a Single Binding

Site for Oxygen

Myoglobin contains 153 amino acids. Myoglobin

contains a porphyrin ring with an iron at its center. A
proximal histidine group (His-93) is attached directly
to iron.
 II. Reversible Binding of a Protein to a Ligand:
Oxygen-Binding Proteins

The reaction is characterized by an equilibrium constant, Ka, such that

The association constant (Ka) provides a measure of the affinity of the ligand L for the protein.
 III. Complementary Interactions Between Proteins and Ligands:
The Immune System and Immunoglobulins

 All vertebrates have an immune system capable of distinguishing molecular “self”

from “nonself” and then destroying those entities identified as nonself.
 In this way, the immune system eliminates viruses, bacteria, and other pathogens
and molecules that may pose a threat to the organism. On a physiological level,
the response of the immune system to an invader is an intricate and coordinated
set of interactions among many classes of proteins, molecules, and cell types.
 However, at the level of individual proteins, the immune response demonstrates
how an acutely sensitive and specific biochemical system is built upon the
reversible binding of ligands to proteins.

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The Immune Response Features a Specialized Array of Cells
and Proteins

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 Self Is Distinguished from Nonself by the Display of Peptides on
Cell Surfaces

The immune system must identify and destroy pathogens, but

it must also recognize and not destroy the normal proteins and cells
of the host organism—the “self.” Detection of protein antigens in the
host is mediated by MHC (major histocompatibility complex) proteins.
MHC proteins bind peptide Non-self of proteins digested in the cell
and present them on the outside surface of the cell.

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Antibodies Have Two Identical Antigen-Binding Sites

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FIGURE 5-21b Immunoglobulin G. (b) A ribbon model of the first complete IgG
molecule to be crystallized and structurally analyzed (PDB ID 1IGT). Although the
molecule has two identical heavy chains (two shades of blue) and two identical
light chains (two shades of red), it crystallized in the asymmetric conformation
shown here. Conformational flexibility may be important to the function of 18
FIGURE 5-22 Binding of IgG to an antigen. To generate an optimal fit for
the antigen, the binding sites of IgG often undergo slight conformational
changes. Such induced fit is common to many protein-ligand
interactions.
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FIGURE 5-23 IgM pentamer of immunoglobulin units. The pentamer is cross-
linked with disulfide bonds (yellow). The J chain is a polypeptide of Mr 20,000
found in both IgA and IgM.
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FIGURE 5-24 Phagocytosis of an antibody-bound virus by a macrophage.
The Fc regions of antibodies bound to the virus now bind to Fc receptors on
the surface of a macrophage, triggering the macrophage to engulf and
destroy the virus.

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Antibodies Bind Tightly and Specifically to Antigen

FIGURE 5-25 Induced fit in the binding of an antigen to IgG.

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 IIII. Protein Interaction Modulated by Chemical
Energy: Actin, Myosin, and Molecular Motors

Organisms move. Cells move. Organelles and macromolecules

within cells move. Most of these movements arise from the activity of a
fascinating class of protein based molecular motors.
Protein-ligand interactions achieve a special degree of spatial
and temporal organization in motor proteins. Muscle contraction
results from choreographed interactions between myosin and actin,
coupled to the hydrolysis of ATP by myosin.

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 The Major Proteins of Muscle Are Myosin and Actin

Myosin consists of two heavy and four light chains, forming a

fibrous coiled coil (tail) domain and a globular (head) domain. Myosin
molecules are organized into thick filaments, which slide past thin
filaments composed largely of actin. ATP hydrolysis in myosin is
coupled to a series of conformational changes in the myosin head,
leading to dissociation of myosin from one F-actin subunit and its
eventual re-association with another, farther along the thin filament.
The myosin thus slides along the actin filaments.

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FIGURE 5-27b Myosin. (b) Cleavage with trypsin and papain separates the
myosin heads (S1 fragments) from the tails.

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FIGURE 5-27c Myosin. (c) Ribbon representation of the myosin S1 fragment
(from coordinates supplied by Ivan Rayment). The heavy chain is in gray, the
two light chains in two shades of blue.
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FIGURE 5-28a The major components of muscle. (a) Myosin
aggregates to form a bipolar structure called a thick filament.

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FIGURE 5-28b The major components of muscle. (b) F-actin is a filamentous assemblage
of G-actin monomers that polymerize two by two, giving the appearance of two filaments
spiraling about one another in a right-handed fashion. 31
FIGURE 5-28c The major components of muscle. (c) Space-filling model of an
actin filament (shades of red) with one myosin head (gray and two shades of
blue) bound to an actin monomer within the filament (from coordinates
supplied by Ivan Rayment).
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Additional Proteins Organize the Thin and Thick Filaments into
Ordered Structures

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 Myosin Thick Filaments Slide along
Actin Thin Filaments
Muscle contraction is stimulated by the
release of Ca2+ from the sarcoplasmic reticulum. The
Ca2+ binds to the protein troponin, leading to a
conformational change in a troponin-tropomyosin
complex that triggers the cycle of actin-myosin
interactions.

FIGURE 5-31 Molecular mechanism of muscle

contraction.

ATP (Adenosine tri-phosphate) is an important molecule found in all living

things. Think of it as the “energy currency” of the cell. If a cell needs to spend
energy to accomplish a task, the ATP molecule splits off one of its three
phosphates, becoming ADP (Adenosine di-phosphate) + phosphate.

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FIGURE 5-32 Regulation of muscle contraction by tropomyosin and troponin.

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