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(2) How to get lecture slides structure.yonsei.ac.kr/ File name: AMB_Ch3 structure.yonsei.ac.kr/ File name: AMB_Ch3 Announcement Advanced Molecular Biology course 2015 is Essential (1) Syllabus Two parts (Dr Cho, Dr Kim) First part covers three themes - Protein Structure and Function (Ch3) - RTK strcuture and anti-cancer monoclonal antibody drugs - Biophysical techniques for experiments Two parts (Dr Cho, Dr Kim) First part covers three themes - Protein Structure and Function (Ch3) - RTK strcuture and anti-cancer monoclonal antibody drugs - Biophysical techniques for experiments
(4) Interviewing with me You may see me during this course if you want My office hours: AM 10:00-11:00 on Thursday How: First, Contact me by or telephone address: You may see me during this course if you want My office hours: AM 10:00-11:00 on Thursday How: First, Contact me by or telephone address: Announcement (continued) (3) Exam and Grading 2 times ( Dr Cho (45%), Dr Kim (45%), attendance(10%) ) Problem types: Short or long answer with figures100% Place: Lecture Room S118A Posting of score in Exam: on the board at room SB134, 2 times ( Dr Cho (45%), Dr Kim (45%), attendance(10%) ) Problem types: Short or long answer with figures100% Place: Lecture Room S118A Posting of score in Exam: on the board at room SB134,
F 1 -ATPase Function is derived from three-dimensional structure ; - Structures define the functions of proteins Only when a protein is in its correct three- dimensional structure, it is able to function Protein Structure and Function
Principles of Biology Living organisms are subject to basic laws of chemistry and physics Major difference between general chemistry and biology; they include more than 70% waters. so biological molecules are always surrounded by waters Four of water’s properties for life –Cohesive behavior –High heat capacity –Expansion upon freezing –Versatility as a solvent H-bonds
Peptide bond is plane! the size of protein; dalton average MW of amino acids in protein : 113
Secondary structure : alpha helix, beta sheet 60% polypeptide chain, H-bond Alpha helix : (n, n+4) carbonyl oxygen, amide hydrogen atom Direction : where is the N-terminal ?
Beta sheet : Parallel, antiparallel pleated sheet Turns : 3-4 residues, glycine, proline common Top view Side view
Motifs : paticular Combinations of Secondary Structures
Structural and functional domains are modules of tertiary structure Structural domain : proline-rich domain, acidic domain, SH3, zinc-finger motif Functional domain : kinase domain, DNA-binding domain Heamagglutinin – Surface protein in influenza virus
Epidermal growth factor
Proteins Associate into multimeric structures and Macromelecular assemblies
RNA polymerase II : 12 subunits (Dr. Roger kornberg) Mediator : 20 subunits
Members of protein families have a common evolutionary ancestor Homologous proteins belongs to a family Non-homologous protein : similar structure, similar function 4 subnits * Oxygen-binding globin Plant BloodMuscle
Folding, Modification, and Degradation of proteins The information for protein folding is encoded in the amino acid sequence Folding of proteins in vivo is promoted by chaperone 95% proteins within cells are in native conformation despite of high concentration ( mg/ml), which favor the precification of proteins in vitro. This can be explained by chaperones. (above 85% protein folding) - Molecular chaperone : bind to exposed hydrophobic regions and stabilize them, thereby preventing these proteins from aggregating and being degraded. (Hsp70+Hsp40, GrpE+DnaK) - Chaperonins directly facilitate the folding of proteins (TriC, GroEL)
TriC ATP X, ADP binding ; bind to misfolded protein ATP binding, GroES ; Releases the folded protein Cavity twofold increase
Chemical Modification of amino acid residues 80% proteins are acetylated ; lifetime control, Nonacetylated protein – short lifetime Nearly every protein in a cell is chemically modified after its synthesis. This may alter the activity, life span, or cellular location of proteins.
Repression by nucleosomes Coiling of DNA around a histone octamer in the nucleosome is now recognized as a cornerstone of transcriptional control. Nucleosomes repress transcription in at least three different ways. First, they occlude sites of protein binding to DNA, thereby interfering with the interaction of activator and repressor proteins, polymerases and transcription factors, DNA-modifying enzymes. Second, chains of nucleosomes can become further coiled or folded, and this higher-order coiling represses transcription of entire chromosomal domains. Finally, interactions of nucleosomes with additional chromosomal proteins in heterochromatin repress gene expression in a hereditary manner6.
Each histone is organized in two domains, a characteristic ‘histone fold’ and an unstructured N-terminal ‘tail’. The histone-fold domains constrain the DNA in a central core particle and, thereby, restrict access of DNA-binding proteins. This histone tail is a flexible amino terminus of residues. Several positively charged lysine side chains in the histone tail may Interact with linker DNA, and the tails of one nucleosome likely interact with Neighboring nucleosomes higher-order coiling.
The histone tail lysine, especially those in H3 and H4, undergo reversible acetylation and deacetylation by enzymes such as CBP (P300) and HDACs In the acetylated form, the positve charge of the lysine e-amino group is neuralized. This eliminate its interaction with a DNA phosphate group. So the greater the acetylation of histone N-terminus, the less likely chromatin is to form condensed 30-nm fibers and possibly higher-order folded structures.
Sites of Histone Tail Modifications Epigenetics edited by Allis et al. (2007)
Distinction between Euchromatic and Heterochromatic Domains H3K9-Me, H3K27- Me H3K4-Me Heterochromatic Hallmarks Euchromatic Hallmarks Epigenetics edited by Allis et al. (2007)
Proteolytic cleavage : blood coagulation, digestion and apoptosis EGF, insulin Protein self-splicing : internal segment is removed. Hedgehog.
Serine is part of a catalytic triad that also includes histidine and aspartate -The three-dimensional structure of chymotrypsin was solved by David Blow in It is synthesized as a single polypeptide, termed Chymotrypsinogen, which is activated by the proteolytic cleavage to yield the three chains. [1GCT.pdb]
-The active site of chymotrypsin, marked by serine 195, lies in a cleft on the surface of the enzyme. -This side chain of serine 195 is hydrogen bonded to the imidazole ring of histidine 57. cleft
Substrate binding Nucleophilic attack Tetrahedral intermediate (acyl-enzyme) Amine is free Water mediated deacylation OH- Attacks the carbonyl carbon Carboxylic acid product Burst phase Steady-state phase
Degradation of protein Lysosomal pathway : extracellular proteins, hydrolytic enzyme and acidic sol’n Ubiquitination : lysine residue attached 76-residue peptide. E1,E2 : thioester bond E3 : specific substrate binding protein isopeptide bond Cytosolic protein ; cyclin Misfolded in ER Immune system
Misfolding not only leads to a loss of the normal function of the protein but also Marks it for proteolytic degradation. The proteolytic fragments filamentous plaques degenerative disease ; Alzheimer’s disease, Parkinson’s disease, mad cow disease Amyloid precursor beta amyloid helix sheet)