lecture 9 12 proteins 2007

Proteins : Proteins Aminoacids Essential aminoacids Structures Modifications Protein Structures & Functions Primary, Secondary and Tertiary Structures Proteins and Diseases Enzyme reactions Classifications Examples and Diseases Enzyme Kinetics Catalysis Inhibitors


The Chemistry of Proteins : The Chemistry of Proteins http://www2.ufp.pt/~pedros/anim/2frame-hben.htm 1962 Nobel Prize in Chemistry Max Perutz, John Kendrew 3D Structures of Hemoglobin and Myoglobin


Amino Acid Configuration : Amino Acid Configuration


Peptide Bond Formation : Peptide Bond Formation


Slide5 : Amino Acids exist as Zwitter-ions


Disulfide Bond Formation : Disulfide Bond Formation


Structural classification of amino acids : Structural classification of amino acids


Slide14 : Amino Acids and One Letter Code


Amino Acids : Amino Acids Isoelectric point or pI: pH at which the net charge is zero. The average of the pKas resulting from gain and loss of H+ by the isoelectric form.


Amino Acids with charged side chains : Amino Acids with charged side chains Isoelectric form


Slide17 : Isoelectric Point and Net Charges


Slide18 : Side Chains, Charges and pKa


Website For Biomolecules : Website For Biomolecules www.bio.cmu.edu/Courses/BiochemMols/ Amino Acids, Proteins, Nucleic Acids Requires the “Chime” Plugin and only works with certain browsers


Primary Structure : Primary Structure


Insulin Primary Structure : Insulin Primary Structure


Posttranslational Modification : Posttranslational Modification


Proteins : Proteins Structural Proteins Collagen, Keratin, actin, spectrin Functional Proteins Enzymes (proteases, glycosidases, helicases) Signaling molecules (transcription factors, Myc, NFkB..) Transport/storage molecules (hemoglobin, transferrin, ferritin, albumin) Antibodies (IgG and IgM)


Proteins - From Sequence to Function : Proteins - From Sequence to Function


Structural Proteins : Structural Proteins Lack catalytic activity Fibrous biomaterials such as hair, nails, skin, cartilage, wool, and silk express structural proteins in abundance


Apoproteins : Apoproteins Non-polypeptide molecules (Prosthetic groups) may be complexed with proteins Iron containing heme-moiety of the oxygen-carrying blood protein hemoglobin Proteins that temporarily lack prosthetic groups (iron-free apolactoferrin), are designated apoproteins


Protein Structures : Protein Structures Amino acid solubility influences polypeptide packing Linear polypeptides form helices and sheets Protein folding is stabilized by higher-order interactions Chaperones assist protein transport by altering folding


Protein Structures : Protein Structures


Protein Shapes : Protein Shapes


Secondary Structure - -helix : Secondary Structure - -helix


-helix - Secondary Structure : -helix - Secondary Structure


-strands, sheets, turns : -strands, sheets, turns


2° Structure Patterns : 2° Structure Patterns


3° Structure - Membrane Proteins : 3° Structure - Membrane Proteins


Slide37 : Structure of pig plasma retinol-binding protein at 1.65 A resolution. Acta Crystallogr., Sect.D v54 pp.1049-1052 , 1998 http://www.pdb.org/pdb/explore.do?structureId=1AQB 3° Structure - Pore Forming Proteins


3° Structure - Pore Forming Proteins : 3° Structure - Pore Forming Proteins Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A. Proc.Natl.Acad.Sci.Usa v102 pp.18932-18937 , 2005 http://www.pdb.org/pdb/explore.do?structureId=2F2B Peter Agre The Nobel Prize in Chemistry 2003 Nobel Lecture Aquaporin Water Channels


Rhodopsin with bound Retinal : Rhodopsin with bound Retinal Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophysical Journal, 83:3097-3112, 2002 Study of rhodopsin based on the x-ray structure with a simulated lipid bilayer.


4° Structure - Myoglobin/Hemoglobin : 4° Structure - Myoglobin/Hemoglobin


4° Structure - Cooperativity : 4° Structure - Cooperativity


4° Structure - Prosthetic Groups : 4° Structure - Prosthetic Groups


4° Structure - Immunoglobulins/Antibodies : 4° Structure - Immunoglobulins/Antibodies


Protein Degradation - Aggregation : Protein Degradation - Aggregation Biosynthesis vs Degradation Proteins that resist degradation causes Alzheimer Disease, Down Syndromes and amyloidoses.


Marfan Syndrome A structural protein problem : Marfan Syndrome A structural protein problem The Marfan syndrome is an inherited, degenerative disorder of the connective tissue, which gives shape and structure to tissues in the body and holds them in place. It affects several organ systems including the ocular system (eyes), the cardiovascular system (heart and blood vessels), and the skeletal system (bones and joints). Mutation in “fibrillin”, a scaffolding protein for connective tissue. More than 50,000 people in the United States have the Marfan syndrome.


Alpha-1 antitrypsin deficiency : Alpha-1 antitrypsin deficiency Alpha-1 antitrypsin (Alpha-1) is produced in the liver Its primary function is to protect the lungs from neutrophil elastase. Neutrophil elastase normally digests diseased or damaged cells. Too much is bad. Most people have two normal copies of the alpha-1 antitrypsin gene. Most Alphas with at least one normal gene can produce enough alpha-1 antitrypsin to stay healthy, especially if they don't smoke. Liver transplant is currently the only option available for advanced disease.


Phenylketonuria : Phenylketonuria Phenylketonuria (PKU) is a human genetic disorder, in which the body lacks phenylalanine hydroxylase, the enzyme necessary to metabolize phenylalanine to tyrosine. Causes brain damage and progressive mental retardation due to accumulation of Phe. Therapy involves severely restricting or eliminating foods high in phenylalanine, such as breast milk, meat, chicken, fish, nuts, cheese and other dairy products. PKU is a leading target for gene therapy since making functional phenylalanine hydroxylase would alleviate the disease. http://www.pdb.org/pdb/explore.do?structureId=1KW0


Tulip, W.R., Varghese, J.N., Baker, A.T., van Donkelaar, A., Laver, W.G., Webster, R.G., Colman, P.M. Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants. J.Mol.Biol. v221 pp.487-497 , 19 : Tulip, W.R., Varghese, J.N., Baker, A.T., van Donkelaar, A., Laver, W.G., Webster, R.G., Colman, P.M. Refined atomic structures of N9 subtype influenza virus neuraminidase and escape mutants. J.Mol.Biol. v221 pp.487-497 , 19 http://www.pdb.org/pdb/explore.do?structureId=5NN9 What are the “extra”, non-peptide groups in the structure?