Haixu Tang School of Inforamtics

Slides:

Advertisements

Similar presentations

Advertisements

Proteins Function and Structure.

Proteins. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 5.4: Proteins have many structures, resulting in a wide range.

Review: Amino Acid Side Chains Aliphatic- Ala, Val, Leu, Ile, Gly Polar- Ser, Thr, Cys, Met, [Tyr, Trp] Acidic (and conjugate amide)- Asp, Asn, Glu, Gln.

FUNDAMENTALS OF MOLECULAR BIOLOGY Introduction -Molecular Biology, Cell, Molecule, Chemical Bonding Macromolecule -Class -Chemical structure -Forms Important.

Protein-a chemical view A chain of amino acids folded in 3D Picture from on-line biology bookon-line biology book Peptide Protein backbone N / C terminal.

Amino Acids and Proteins 1.What is an amino acid / protein 2.Where are they found 3.Properties of the amino acids 4.How are proteins synthesized 1.Transcription.

Proteins Function and Structure. Proteins more than 50% of dry mass of most cells functions include – structural support – storage, transport – cellular.

Chapter 3 The Chemistry of Organic Molecules

Protein Structure FDSC400. Protein Functions Biological?Food?

You Must Know How the sequence and subcomponents of proteins determine their properties. The cellular functions of proteins. (Brief – we will come back.

Proteins. The central role of proteins in the chemistry of life Proteins have a variety of functions. Structural proteins make up the physical structure.

Protein Structural Prediction. Protein Structure is Hierarchical.

Proteins account for more than 50% of the dry mass of most cells

Proteins account for more than 50% of the dry mass of most cells

What are proteins? Proteins are important; e.g. for catalyzing and regulating biochemical reactions, transporting molecules, … Linear polymer chain composed.

Bioinformatics: Practical Application of Simulation and Data Mining Protein Folding I Prof. Corey O’Hern Department of Mechanical Engineering & Materials.

Amino Acids & Side Groups Polar Charged ◦ ACIDIC negatively charged amino acids  ASP & GLU R group with a 2nd COOH that ionizes* above pH 7.02nd COOH.

NOTES: 2.3 part 2 Nucleic Acids & Proteins. So far, we’ve covered… the following MACROMOLECULES: ● CARBOHYDRATES… ● LIPIDS… Let’s review…

The Structure and Function of Macromolecules Chapter Proteins.

Chapter 3 Proteins.

Proteins Tertiary Protein Structure of Enzyme Lactasevideo Video 2.

Arginine, who are you? Why so important?. Release 2015_01 of 07-Jan-15 of UniProtKB/Swiss-Prot contains sequence entries, comprising

Proteins Fibrous 1o structure amino acid sequence 2o structure

Introduction to Molecular Neurobiology

Introduction to Protein Structure

PROTEINS LEVELS OF PROTEIN STRUCTURE Central Carbon Atom 3.

Proteins account for more than 50% of the dry mass of most cells

Protein Structure and Properties

Proteins The most important biochemicals in cells are proteins (enzymes) Protect organisms from disease Extract energy from food Move essential cellular.

The Structure and Function of Large Biological Molecules

Transport proteins Transport protein Cell membrane

Cathode (attracts (+) amino acids)

Protein Structure FDSC400. Protein Functions Biological?Food?

Standards Distinguish among proteins, carbohydrates, lipids, and nucleic acids. Identify the major structural components and functions of the four major.

Proteins account for more than 50% of the dry mass of most cells

Figure 3.14A–D Protein structure (layer 1)

Chemistry 121 Winter 2016 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)

Proteins account for more than 50% of the dry mass of most cells

The forces at work on proteins/ glutamic acid and valine

Chapter 3 Proteins.

Amino acids R-groups non-polar polar acidic basic proteins

Fig. 5-UN1  carbon Amino group Carboxyl group.

Packet #9 Supplement.

The Structure and Function of Macromolecules

Amino Acids Amine group -NH2 Carboxylic group -COOH

Packet #9 Supplement.

Amino acids R-groups non-polar polar acidic basic proteins

Amino acids R-groups non-polar polar acidic basic proteins

Proteins account for more than 50% of the dry mass of most cells

Proteins Genetic information in DNA codes specifically for the production of proteins Cells have thousands of different proteins, each with a specific.

The 20 amino acids.

Chapter Three Amino Acids and Peptides

Tay Sachs vs Sickle cell

Levels of Protein Structure

How to Test an Assertion

The 20 amino acids.

Chapter 18 Naturally Occurring Nitrogen-Containing Compounds

The Chemical Building Blocks of Life

Proteins Fibrous 1o structure amino acid sequence 2o structure

Example of regression by RBF-ANN

Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes 2. Proteins are.

“When you understand the amino acids,

Justin Spiriti Zuckerman Lab MMBioS meeting 5/22/2014

The Three-Dimensional Structure of Proteins

Fig. 3 Organization of the active site of DHHC20.

Presentation transcript:

Haixu Tang School of Inforamtics Protein structures Haixu Tang School of Inforamtics

A covalent peptide bond

Protein conformation is specified by tts Amino Acid sequence Steric interactions Weak non-covalent bonds hydrogen bonds ionic bonds van der Waals attractions Hydrophobic interaction distribution of its polar and nonpolar amino acids

Protein folding: lowest energy conformation

Protein denaturalization

Visualizing protein conformations Protein structures in atomic level Protein Data Bank (PDB) http://www.rcsb.org Pymol: http://pymol.sourceforge.net/ Rasmol: http://www.umass.edu/microbio/rasmol/

Protein secondary structure

Secondary structure prediction Prefer a-helix: Ala, Leu, Met, Phe, Glu, Gln, His, Lys, Arg (sidechains cover and protect the backbone H-bonds) Prefer b-sheet: Tyr, Trp, Phe, Ile, Val, Thr, Cys (large bulky sidechains) Disrupt secondary structure: Gly, Pro, Ser, Asp, Asn (small, restrained, or sidechain hydrogen bonds)

Coiled coil

Protein Domains Independent structural unit Independent function Independent folding Independent evolve

Protein families

Class Folds Super-families Families Protein structural classification (SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/) Class Folds Super-families Families

Sulfur-sulfur (disulfur) bonds

Assembly of Large Structures

Experimental determination of protein structures X-ray crystallography NMR (Nuclear Magnetic Resonance) Spectroscopy

X-ray crystallography

NMR spectrum