The document discusses a seminar presentation on protein modeling. It covers topics like molecular modeling techniques, protein structure prediction, and applications of molecular modeling. The main points are: - Molecular modeling techniques like molecular mechanics and quantum mechanics are used to model protein structures and properties. - Protein structure prediction aims to determine a protein's 3D structure from its amino acid sequence. This remains a challenging problem. - Knowing a protein's structure provides insight into its function and allows designing mutations or drugs to modify the protein. - Molecular modeling has wide applications in research areas like chemistry, biology and physics. It is used to simulate molecular behavior in chemical and biological systems.

2. SRI PARAMAKALYANI COLLEGE
ALWARKURCHI-627412
S. MOHAMED MUSTHAFA
II M.SC MICROBIOLOGY
REG NO: 20201232516111
DATE 11.12.2021
DAY SATURDAY
Submitted to
Miss.M.MUTHUSELVI
ASSISTANT PROFESSOR OF MICROBIOLOGY
SPKC,ALWARKURCHI
BIOINFORMATICS AND BIOSTASTICS
PROTEIN MODELING

3. CONTENTS OF SEMINAR
 INTRODUCTION
 MOLECULAR MODELING
 TYPES OF MOLECULAR MODELING
 APPLICATION OF MOLECULAR MODELING
 PROTEINS IN BRIEF
 PURPOSE OF PROTEIN STRUCTURE PREDICTION
 TYPES OF PSP
 CONCLUTION

4. INTRODUCTION
 Proteins are made up of amino acids.
 Protein Structural Organization.
I. Primary
II. Secondary
III. Tertiary
IV. Quaternary
 Each protein folds into a unique three-dimensional structure that enables it to carry out its biological
function.
 Predicting the 3D structure of proteins from their amino acid sequences remains a challenging problem.

5. MOLECULAR MODELING
 The science (or art) of representing molecular structures numerically and simulating their behavior with
the equations of quantum and classical physics.
 Combination of computational chemistry and computer graphics.
 Allows scientists to generate and present molecular data including geometries (bond lengths, bond angles,
torsion angles), energies (heat of formation, activation energy, etc.), electronic properties (moments,
charges, ionization potential, electron affinity), spectroscopic properties (vibrational modes, chemical
shifts) and bulk properties (volumes, surface areas, diffusion, viscosity, etc.).

7. TYPES OF MOLECULAR MODELING
 The two most common computational methods
A. Molecular mechanics
B. Quantum mechanics
 Both these methods produce equations for the total
energy(E) of the structure.

8. MOLECULAR MECHANICS
• Calculation of energy of atoms, force on atoms and
their resulting motion.
• Used to model the geometry of the molecule,
motion of molecule and to get the global minimum
energy structure.
CONSIDER A MOLECULE AS SYSTEM OF RIGID BALLS CONNECTED
VIA SPRINGS
• Depends strongly on concepts of bonding
• Follows the Newtonian laws
• Neglect the electronic degrees of freedom

9. QUANTUM MECHANICS
 Provides information about both nuclear position and distribution.
 Based on study of arrangement and interaction of electrons and
nuclei of a molecular system.
 It does not require the use of parameters similar to those used in
molecular mechanics.
 It is based on the wave properties of electrons and all material
particles.

10. APPLICATION OF MOLECULAR MODELING
 
To calculate the value of potentials, electron affinities ,heat
of formation, dipole moment and other physical
properties
 To find the electron density in a structure
 To determine the points at which a structure will react with
electrophiles and nucleophiles
 To determine the shape and electron density of a
molecule

11. PROTEINS IN BRIEF
 Protein is an essential macronutrient that acts to build, maintain, regulate, and repair body tissues. More specifically, essential functions of
protein in the body include:
 serving as enzymes to catalyze reactions in processes such as metabolism, DNA replication, and digestion [Shils 2006]
 serving as certain hormones and antibodies
 regulating essential body processes including distribution of water in the body, nutrient transport, and muscle contractions
 helping maintain the acid-base balance
 providing a source of energy - about 4 calories per gram
 helping keep skin, hair, and nails healthy.
 The Dietary Reference Intake guidelines recommend that protein should make up 5% to 20% of the calories consumed each day by children 1-
3 years old, and 10-30% of total energy intake for 4-18 year olds.
 Protein is a chemical compound that contains the same atoms as carbohydrate and fat - carbon (C), hydrogen (H) and oxygen (O) - but protein
also contains nitrogen (N) atoms. These C, H, O and N atoms are arranged into amino acids, which are linked into chains to form proteins. The
sizes and structures of proteins vary widely in complexity, which enables proteins to play a variety of functions in the cell. For example, the
structure of the amino acid lysine is shown below.

12. PROTEIN STRUCTURE
 Protein structure is the three-dimensional
arrangement of atoms in an amino acid-
chain molecule. Proteins are polymers –
specifically polypeptides – formed from sequences
of amino acids, the monomers of the polymer.
 A single amino acid monomer may also be called
a residuProteins form by amino acids
undergoing condensation reactions, in which the
amino acids lose one water
molecule per reaction in order to attach to one
another with a peptide bond.
 By convention, a chain under 30 amino acids is
often identified as a peptide, rather than a
protein.
 To understand the functions of proteins at a
molecular level, it is often necessary to
determine their three-dimensional structure.
 This is the topic of the scientific field
of structural biology, which employs techniques
such as X-ray crystallography, NMR

14. LEVELS OF PROTEIN STRUCTURE
 PRIMARY STRUCTURE
 SECONDARY STRUCTURE
 TERTIARY STRUCTURE
 QUATERNARY STRUCTURE

16. TYPES OF PSP
Explaining phenotype of existing mutations (experimental or patient-derived)
 Designing mutants to disrupt or alter specific functions (leaving others unaffected)
 Hints at function
 Drug design (at high sequence identity)
 Hypothesis generation

17. CONCLUSION
Having a protein structure provides a greater level of understanding of how a protein works, which can
allow us to create hypotheses about how to affect it, control it, or modify it.
For example:
knowing a protein's structure could allow you to design site-directed mutations with the intent of changing
function
Molecular modeling is rapidly growing according to its applications in many areas of research. It is now widely
used to study the molecular structure of large systems and in physics, chemistry, and biology. Molecular
modeling is used to simulate the molecular behavior in chemical or biological systems