COURSE TITLE: Chemistry of

Macromolecules
COURSE CODE: BCH 203
Lecturer: Mrs Famutimi Olufemi

A TERM PAPER ON
PROTEIN STRUCTURE
AND DISEASES
BY
OGUNDELE
OLUWADAMILARE
OLANREWAJU
BCH/2021/144
INTRODUCTION
Protein structures are intricate arrangements of amino acids that form the building blocks of
living organisms. These structures are fundamental to various biological processes due to the
diverse function’s proteins perform. Proteins serve ass enzymes, catalysts for biochemical
reactions; structural components, providing support to cells and tissues; signaling molecules,
transmitting messages within and between cells; and transporters, facilitating the movement
of substances across membranes. The precise three-dimensional conformations of proteins are
essential for their proper functioning, and deviations from their native structures can lead to
dysfunction and disease. Understanding protein structures is key to unravelling the
complexities of cellular mechanisms and developing insights into the molecular basis of
health and pathology.
The intricate relationship between protein structures and the development of diseases lies in
the susceptibility of these structures to alterations, often resulting in functional abnormalities.
Proteins, with their specific three-dimensional configurations, play pivotal roles in
maintaining cellular homeostasis. However, genetic mutations, environmental factors, or
other stressors can induce changes in protein structures, leading to misfolding, aggregation,
or loss of function. Such structural anomalies are implicated in the onset and progression of
various diseases.
For instance, misfolded proteins are associated with neurodegenerative disorders like
Alzheimer’s and Parkinson’s, where aggregates contribute to neuronal damage. In certain
cancers, mutations in proteins can disrupt regulatory pathways, promoting uncontrolled cell
growth. Understanding the link between protein structures and diseases is crucial for
identifying potential therapeutic targets, designing interventions to restore normal protein
function, and advancing the field of precision medicine. Investigating the structural basis of
diseases provides insights into diagnostic methods, drug development, and ultimately,
strategies to mitigate the impact of diverse pathological conditions.

AMINO ACIDS

Amino acids are the building block of proteins. Amino acids are important organic
compounds that contain amine (-NH2 ) and Carboxyl (-COOH) functional groups, along with
a side-chain (R group) that is specific for each amino acid (Figure 1). Twenty different amino
acids are commonly found in proteins.
Figure 1 :

All these 20 common amino acids are α-amino acids except proline and their general
structure is shown below. They have a carboxyl group and amino group which are covalently
bonded to a α-carbon atom. They differ from each other in their side chain R groups. Since,
the remaining structure are same therefore properties of these amino acids are primarily
determined by the side chain groups. The nature of these side chain maybe polar, nonpolar
(aliphatic), hydrophilic, hydrophobic, acidic, basic, and aromatic. These amino acids have
been abbreviated using either three letter word or one letter word.
 Proteins
Proteins are made from amino acids and therefore always contain the elements carbon,
hydrogen, oxygen, and nitrogen, and in some cases sulphur. Some proteins form complexes
with other molecules containing phosphorus, iron, zinc, and copper. Proteins are
macromolecules of high Mr (relative formula mass or molecular mass), typically between
several thousands and several millions, consisting of chains of amino acids. They are
polymers and amino acids are the monomers. There are 20 different amino acids which are
commonly found in naturally occurring proteins. The potential variety of proteins is
unlimited because the sequence of amino acids in each protein is specific for that protein and
is genetically controlled by the DNA of the cell in which it is made. Proteins are the most
abundant organic molecules to be found in cells and form over 50% of their total dry mass.
They are an essential component of the diet of animals and may be converted to both fat and
carbohydrate by the cells. Their diversity enables them to display a great range of structural
and metabolic activities within the organism.

Size of protein molecules

Simple peptides containing two, three or four amino acid residues are called di-, tri- and
tetrapeptides respectively. Polypeptides are chains of many amino acid residues (up to
several thousand — table 3.6). A protein may possess one or more polypeptide chains.

Number of Protein Molecular Mass Amino Acids Number of

polypeptide chains
Ribonuclease 12640 124 1
Lysozyme 13930 129 1
Myoglobin 16890 153 1
Haemoglobin 64500 574 4
TMV About 400 000 000 About 336 500 2130

Structure of proteins
Each protein possesses a characteristic three-dimensional shape, its conformation. There are
four separate levels of structure and organisation as follows.

1. Primary structure
The primary structure of a protein involves the linear sequence of amino acids, forming the
backbone of the protein molecule. Any changes or mutations in this sequence can have
profound effects on the protein’s structure and function.

The primary structure is the sequence of amino acids in a polypeptide chain. The first person
to work out the complete amino acid sequence of a protein was Fred Sanger, working at the
Cavendish laboratory in Cambridge, where Watson and Crick also determined the structure of
DNA. He worked with the hormone insulin, the smallest protein he could find. It took ten
years, and the results were published in 1953. Max Perutz, another great molecular biologist
of the Cavendish, recalls 'it caused a sensation, because it proved for the first time that protein
has a specific arrangement of amino acids along its chain.' Sanger was awarded the Nobel
prize for his work in 1958 (and has since won a second for work on nucleic acids). Insulin is a
protein of 51 amino acids. It is made of two polypeptide chains held together by disulphide
bridges.

2. Secondary Structure
The secondary structure of a protein refers to the local folding patterns within the polypeptide
chain. Common secondary structures include alpha helices and beta sheets, stabilized by
hydrogen bonds between amino acids.
The two main types of secondary structures are:

1. Alpha Helix: A right-handed coil formed by hydrogen bonding between the carbonyl
oxygen of one amino acid and the amide hydrogen of an amino acid four residues
away. This helical structure provides stability to the protein.

2. Beta Sheet: A structure where adjacent polypeptide strands are connected by hydrogen
bonds, forming a sheet-like arrangement. Beta sheets can be parallel or antiparallel,
contributing to the protein’s overall stability.

These secondary structures result from interactions between amino acid residues and play a
crucial role in determining a protein’s three-dimensional conformation and, consequently, its
function.

3. Tertiary structure
Usually, the polypeptide chain bends and folds extensively, protein's forming a
tertiary precise, structure compact and 'globular' it is maintained shape. This is by
the interaction of the four types of bonds already discussed, namely ionic,
hydrogen and disulphide bonds as well as hydrophobic interactions. The latter
are quantitatively the most important and occur when the protein folds to shield
hydrophobic side groups from the aqueous surroundings, at the same time
 exposing hydrophilic side chains, as described above. The tertiary structure of a
protein can be determined by X-ray crystallography.

By early 1959, and after many years' work, John Kendrew and Max Perutz had
built the first atomic model of myoglobin showing secondary and tertiary
structures using this technique. They received the Nobel prize for their work in
1962.

4. Quaternary Structure
Many highly complex proteins consist of more than one polypeptide chain. The separate
chains are held together by hydrophobic interactions and hydrogen and ionic bonds. Their
precise arrangement is known as the quaternary structure. Haemoglobin shows such a
structure. It is the red oxygen-carrying pigment found in the red blood cells of vertebrates.
It consists of four separate polypeptide chains of two types, namely two α chains and two ß
chains. These resemble myoglobin in structure. The two α chains each contain 141 amino
acids, while the two chains each contain 146 amino acids. The complete structure of
haemoglobin was worked out by Kendrew and Perutz.
As is typical of globular proteins, its hydrophobic side chains point inwards to the
centre of the molecule, and its hydrophilic side chains face outwards, making it soluble in
water. A mutation which causes one of the hydrophilic amino acids to be replaced by a
hydrophobic amino acid, thereby reducing its solubility, is responsible for the disease sickle
cell anaemia.

Protein Folding
Protein folding is the complex process by which a linear chain of amino acids, known as a
polypeptide, acquires its three-dimensional functional and biologically active structure. This
process is critical for a protein to carry out its specific biological functions within cells.
The primary structure of a protein, dictated by the sequence of amino acids encoded in its
corresponding gene, serves as the starting point for folding. The folding process is influenced
by various interactions among amino acid residues, including:

1. Hydrophobic Interactions: Nonpolar amino acids tend to cluster together in the

protein’s interior away from water, stabilizing the structure.

2. Hydrogen Bonds: Formed between the hydrogen atom of one amino acid and the
oxygen or nitrogen atom of another, contributing to the folding pattern.

3. Disulfide Bonds: Covalent bonds between the sulphur atoms of two cysteine residues,
providing additional stability to the protein structure.
 4. Ionic Interactions: Attraction or repulsion between positively and negatively charged
amino acid side chains, influencing the folding process.

The protein folds into specific secondary structures like alpha helices and beta sheets, which
further arrange into a unique tertiary structure. In some cases, multiple polypeptide chains
(subunits) come together to form the quaternary structure.
Protein folding is a highly orchestrated and regulated process within cells. Chaperone
proteins assist in the folding of nascent polypeptides, preventing misfolding or aggregation.
When proteins fail to fold correctly, it can lead to functional deficits or even contribute to the
development of diseases, including neurodegenerative disorders.

Importance of Protein Folding and Conformation on their Functions

Protein folding and conformation are crucial for the proper functioning of proteins,
influencing their stability, specificity, and functionality. The precise folding and conformation
of proteins are fundamental to their biological activity. Any deviations from the correct
folding patterns can lead to loss of function or even contribute to pathological conditions.
1. Structure-Function Relationship:
Precision in Interaction: The intricate three-dimensional folding of proteins is directly
correlated with their biological functions. The specific arrangement of amino acids
dictates how a protein interacts with other molecules, be it substrates, cofactors, or other
proteins.
2. Stability:
Maintaining Structural Integrity: The folding process is essential for maintaining the
structural stability of proteins. Hydrophobic interactions, hydrogen bonds, and disulfide
bridges formed during folding contribute to the robustness of the protein structure.
3. Active Site Formation:
Catalytic Efficiency: Enzymes, a class of proteins, rely on precise folding to form active
sites. The correct folding brings catalytic residues into proximity, enhancing the
efficiency of chemical reactions.
4. Interaction with Ligands:
Selective Binding: Proteins often function by binding to specific ligands. The folding
pattern ensures the formation of binding sites that selectively recognize and interact with
these ligands, contributing to cellular signalling, transport, and regulation.
5. Cellular Localization:
Spatial Organization: Proper folding is crucial for a protein to adopt the correct
conformation for its intended cellular location. The cell’s spatial organization relies on
 proteins being accurately folded to function in specific compartments or to be
transported to designated destinations.
6. Disease and Misfolding:
Pathological Implications: Misfolding of proteins is implicated in numerous diseases.
The failure to achieve the correct folded state can lead to protein aggregation, a
hallmark of conditions like Alzheimer’s and Parkinson’s diseases, underscoring the
critical role of proper folding in maintaining cellular health.

In conclusion, the intricacies of protein folding, and conformation extend across multiple
layers, from molecular precision to systemic functionality. Understanding these processes is
essential not only for unravelling the mysteries of cellular biology but also for advancing
therapeutic approaches in the treatment of various diseases.

Techniques for Studying Protein Structures

1. X-ray Crystallography:
a. Principle: X-ray diffraction patterns generated by crystallized proteins are
used to determine the electron density of the protein, unveiling its three-
dimensional structure.
Advantages:
 High resolution
 suitable for large proteins and complexes.
Limitations:
 Requires protein crystallization, which may be challenging for some
proteins.
Contribution:
 Provides high-resolution structural details by revealing the electron
density map of crystallized proteins.
 It is particularly valuable for determining the arrangement of atoms
within a crystal lattice.
Application:
 Ideal for large proteins and complexes,
 Aiding drug design by identifying potential binding sites.
2. Nuclear Magnetic Resonance (NMR) Spectroscopy:
Principle: Detection of nuclear magnetic resonance signals from isotopically
labelled proteins in solution to derive structural information.
Advantages:
 Suitable for studying dynamic structures in solution.
 doesn’t require crystallization.
Limitations:
 Limited to smaller proteins
 lower resolution compared to X-ray crystallography.
Contribution:
  Offers insights into the dynamic aspects of proteins in solution.
 NMR provides atomic-level details especially for smaller
proteins.
 helps understand conformational changes.
Application:
Useful for studying protein-protein interactions, structural dynamics,
and intrinsically disordered proteins.

3. Cryo-Electron Microscopy (Cryo-EM):

Principle: Electron micrographs of frozen-hydrated specimens are used to reconstruct a 3D
model of the protein.
Advantages:
o High resolution,
o applicable to large complexes,
o doesn’t require crystallization.
Limitations:
o Sample preparation challenges,
o lower resolution compared to X-ray crystallography for some applications.
Contribution:
o Allows high-resolution imaging of large protein complexes and provides
structural information without the need for crystallization.
o Cryo-EM has revolutionized the study of macromolecular structures.
Application: Essential for visualizing dynamic biological processes, membrane proteins,
and large molecular complexes.

3. Fluorescence Spectroscopy:
Principle: Measurement of fluorescence emission to study protein conformational
changes and interactions.
Advantages: Sensitive, applicable to real-time studies.
Limitations: Limited structural resolution, dependence on fluorophore placement.
Contribution: Measures changes in fluorescence emission to understand protein
conformational changes and interactions. Fluorescent probes can be strategically placed for
studying specific regions of a protein.
Application: Useful for real-time monitoring of protein folding, ligand binding, and
studying structural changes in response to environmental factors.
5. Mass Spectrometry (MS):
Principle: Mass-to-charge ratios of ionized protein fragments are measured, providing
information on composition and structure.
Advantages:
 Useful for studying protein interactions.
 post-translational modifications.
Limitations: Limited in providing high-resolution structural details.
Contribution: Provides information on protein composition, post-translational
modifications, and protein interactions. Structural information can be inferred by analysing
the mass-to-charge ratios of ionized protein fragments.
Application: Valuable for studying protein dynamics, post-translational modifications, and
mapping protein-protein interactions.

Protein Misfolding and Diseases

Errors in protein folding can lead to misfolded proteins, which can have detrimental effects
on cellular function. Protein folding is a highly intricate process guided by the sequence of
amino acids in a polypeptide chain, and several factors can contribute to misfolding:

1. Genetic Mutations:
Point Mutations: Alterations in the DNA sequence can result in a change in a single amino
acid, affecting the folding process.
Insertions or Deletions: Shifts in the reading frame can lead to the insertion or deletion of
amino acids, disrupting the correct folding pattern.

2. Environmental Factors:
Temperature and pH: Changes in environmental conditions, such as elevated temperatures
or extremes in pH, can destabilize protein structures, promoting misfolding.
Chemical Agents: Exposure to certain chemicals or toxins can induce protein misfolding by
interfering with the folding process.

3. Chaperone Deficiency:
Chaperone Proteins: Chaperones assist in the correct folding of proteins. Deficiencies in
chaperone function can lead to the accumulation of misfolded proteins.
 Heat Shock Response: Cellular stress, such as heat shock, can overwhelm the chaperone
machinery, leading to the misfolding of proteins.

4. Post-Translational Modifications:
Aberrant Modifications: Improper addition of functional groups or post-translational
modifications can hinder the correct folding of proteins, affecting their structure and function.

5. Protein Overexpression:
Overproduction: Excessive production of a protein can overwhelm the cellular folding
machinery, leading to the accumulation of misfolded proteins.

6. Aging:
Accumulation of Damage: Over time, cells may accumulate damage to molecular
components, including proteins, which can contribute to misfolding.

When proteins misfold, several outcomes can occur:

Loss of Function: Misfolded proteins may lose their normal biological activity. This
can be particularly critical if the misfolded protein is an enzyme or involved in a
signalling pathway.
Toxic Aggregation: Misfolded proteins are prone to aggregation, forming clumps or
aggregates. These aggregates can interfere with cellular processes and may be toxic to
cells, contributing to various neurodegenerative diseases.
Cellular Stress Responses: Cells often activate stress response mechanisms, such as
the unfolded protein response (UPR), to cope with the presence of misfolded proteins.
Prolonged activation of these responses can lead to cell dysfunction or death.
Disease Association: Misfolded proteins are implicated in numerous diseases,
including Alzheimer’s, Parkinson’s, Huntington’s, and prion diseases. The
accumulation of misfolded proteins is a common feature of these disorders.
Understanding the mechanisms of protein misfolding is crucial for developing strategies to
mitigate its effects and potentially treat diseases associated with misfolded proteins.

Several diseases are associated with protein misfolding, where proteins adopt abnormal
conformations and may form aggregates. These diseases are often referred to as protein
misfolding disorders. Here are some notable examples:

1. Alzheimer’s Disease:
 Protein: Amyloid-beta (Aβ) and Tau proteins.
Characteristics: Formation of extracellular plaques (Aβ) and intracellular neurofibrillary
tangles (Tau) in the brain, leading to neurodegeneration.

2. Parkinson’s Disease:
Protein: Alpha-synuclein.
Characteristics: Aggregation of alpha-synuclein into Lewy bodies, which are abnormal
protein clumps in neurons. This disrupts normal cellular function and contributes to
neurodegeneration.

3. Huntington’s Disease:
Protein: Huntingtin.
Characteristics: Expansion of a CAG repeat in the huntingtin gene leads to the production
of a mutant huntingtin protein. This misfolded protein forms aggregates, especially in
neurons, causing neurodegeneration.

4. Prion Diseases (e.g., Creutzfeldt-Jakob Disease):

Protein: Prion protein (PrP).
Characteristics: Normal PrP misfolds into an abnormal, infectious form, leading to the
accumulation of misfolded proteins in the brain. Prion diseases are transmissible and result in
severe neurological symptoms.

5. Cystic Fibrosis:
Protein: Cystic fibrosis transmembrane conductance regulator (CFTR).
Characteristics: Mutations in the CFTR gene lead to misfolding of the CFTR protein,
affecting its transport function. This results in the production of thick, sticky mucus, causing
respiratory and digestive issues.

7. Type 2 Diabetes:
Protein: Amylin.
Characteristics: Misfolding and aggregation of amylin in pancreatic islets contribute to the
formation of amyloid deposits. This impairs insulin secretion and worsens diabetes.

Alterations In Specific Proteins

 1. Beta-Amyloid (Aβ) in Alzheimer’s Disease:
Alterations:
- Misfolding and aggregation of Aβ peptides, leading to the formation of
extracellular plaques.
Pathological Consequences
o Disruption of synaptic function and impairment of neurotransmission.
o Activation of microglia and neuroinflammatory responses.
o Formation of neurofibrillary tangles composed of hyperphosphorylated tau
proteins, contributing to neuronal death.
o Impaired clearance mechanisms and accumulation of toxic Aβ oligomers.

2. Alpha-Synuclein in Parkinson’s Disease:

Alterations:
Misfolding and aggregation of alpha-synuclein into Lewy bodies.
Pathological Consequences:
 Disruption of cellular membranes and vesicular trafficking.
 Impaired function of proteasomal and lysosomal degradation systems.
 Generation of toxic species causing oxidative stress.
 Selective degeneration of dopaminergic neurons in the substantia nigra, leading to
motor symptoms.
3. Huntingtin in Huntington’s Disease:
Alterations:
Expansion of polyglutamine (CAG) repeat in huntingtin, resulting in misfolding and
aggregation.
- Pathological Consequences:
 Formation of intracellular inclusion bodies containing aggregated huntingtin.
 Dysregulation of protein degradation pathways, including the ubiquitin-proteasome
system and autophagy.
 Disruption of cellular homeostasis and eventual death of neurons, particularly in the
striatum.

4. Prion Protein (PrP) in Prion Diseases:

Alterations:
Conversion of normal PrPC to misfolded PrPSc.
Pathological Consequences:
  Accumulation of misfolded prion proteins in the brain.
 Ongoing conversion of normal PrPC to the infectious PrPSc form.
 Formation of amyloid plaques and spongiform changes in brain tissue.
 Rapid progression of neurodegeneration and cognitive decline.

Therapeutic Interventions Targeting Protein Structures

There are different strategies to intervene with protein structures, depending on the nature and
mechanism of the disease. Some of the potential therapeutic interventions are:
 Targeted protein degradation (TPD): This approach aims to selectively eliminate
disease-causing proteins by harnessing the natural mechanisms of the cell, such as the
ubiquitin-proteasome system (UPS) or the lysosome pathway. TPD agents, such as
proteolysis-targeting chimeras (PROTACs), can recruit specific E3 ligases to
ubiquitinate and degrade the target protein. TPD has several advantages over
conventional small molecule inhibitors, such as overcoming drug resistance, reducing
side effects, and expanding the druggable space1.
 Protein stabilization: This approach aims to prevent or reverse the misfolding or
aggregation of proteins by stabilizing their native or functional conformation. Protein
stabilizers, such as pharmacological chaperones, can bind to the target protein and
enhance its folding, stability, or activity. Protein stabilization can be beneficial for
diseases caused by loss-of-function mutations, such as lysosomal storage disorders, or
by toxic protein aggregates, such as amyloidoses2.
 Protein delivery: This approach aims to deliver therapeutic proteins to the site of
action, either by direct injection or by gene therapy. Protein delivery can be used to
replace or supplement deficient or defective proteins, such as enzymes, hormones, or
antibodies. Protein delivery can also be used to modulate the expression or activity of
other proteins, such as transcription factors, growth factors, or cytokines. Protein
delivery faces several challenges, such as stability, immunogenicity, and targeting 3.
These are some of the potential therapeutic interventions targeting protein structures to treat
or prevent diseases. However, there are still many obstacles and limitations to overcome,
such as specificity, selectivity, efficacy, safety, and delivery. Therefore, more research and
development are needed to optimize and validate these approaches for clinical applications.

Case Studies
There are many case studies of successful applications of protein structure knowledge in
disease treatment. Here are some examples:
 Cystic fibrosis (CF): CF is a genetic disorder caused by mutations in the CF
transmembrane conductance regulator (CFTR) protein, which is responsible for
transporting chloride ions across cell membranes. The most common mutation,
F508del, causes the protein to misfold and be degraded by the cell. Researchers have
used protein structure knowledge to design small molecules that can correct the
folding and function of F508del-CFTR, such as VX-809 and VX-661. These
molecules act as pharmacological chaperones, binding to the mutant protein and
stabilizing its conformation. In combination with other drugs that enhance the activity
 of CFTR, such as VX-770 and VX-445, these molecules have shown significant
clinical benefits for CF patients12.
 HIV/AIDS: HIV is a retrovirus that infects and destroys CD4+ T cells, leading to
immunodeficiency and opportunistic infections. HIV has several key proteins that are
essential for its replication and survival, such as reverse transcriptase, protease,
integrase, and envelope glycoprotein. Researchers have used protein structure
knowledge to design inhibitors that target these proteins and block their function, such
as AZT, indinavir, raltegravir, and enfuvirtide. These inhibitors have been used in
combination therapy, known as highly active antiretroviral therapy (HAART), to
suppress viral load and improve immune function in HIV patients34.
 Cancer: Cancer is a group of diseases characterized by uncontrolled cell growth and
invasion. Cancer cells have various genetic and epigenetic alterations that affect the
expression and function of many proteins involved in cell cycle, apoptosis, signal
transduction, angiogenesis, and metastasis. Researchers have used protein structure
knowledge to design drugs that target these proteins and modulate their activity, such
as imatinib, trastuzumab, vemurafenib, and olaparib. These drugs have shown
remarkable efficacy and specificity for certain types of cancer, such as chronic
myeloid leukemia, breast cancer, melanoma, and ovarian cancer

Conclusion
Protein structure is a key determinant of protein function and regulation. Understanding
the relationship between protein structure and disease is crucial for developing novel and
effective therapeutic interventions. In this paper, we have reviewed some of the current
strategies and challenges of targeting protein structures to treat or prevent various
diseases, such as cystic fibrosis, HIV/AIDS, and cancer. We have also discussed some of
the successful applications of protein structure knowledge in drug design and discovery. I
hope that this paper will provide a useful overview and insight for researchers and
students interested in this fascinating and important field of study.

References
1. Tayyab S, Nasrulhaq A. A journey from amino acids to proteins. University of Malaya
press. 2006.
2. Cox MM, Nelson DL. Lehninger Principles of Biochemistry 2011. Fifth Edition.
WH Freeman and Company. New York (USA).
3. Monod J, Wyman J, Changeux JP. On the nature of allosteric transitions: A plausible
model. J M Biol. 1965; 12: 88-118\
4. In silico Analyses of Gene Expression and Protein Structure/Function and
Applications in Disease (uic.edu)
5. D.J. Taylor, N.P.O Green, G.W. Stout. Biological Science 1&2
6. Biomedicines | Special Issue : Protein Structure, Function and Dynamics in Diseases
and Therapeutics (mdpi.com)
7. https://link.springer.com/article/10.1007/s11030-023-10606-w
8. Neurodegenerative diseases distinguished through protein-structure analysis
(nature.com)