marie-véronique clement associate professor yong loo lin school of medicine
DESCRIPTION
Protein structure and function Part - I. Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine NUS Graduate School for Integrative Science and Engineering Department of Biochemistry National University of Singapore 8 Medical Drive, MD 7 #03-15 Singapore 117597 - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/1.jpg)
Marie-Véronique CLEMENTAssociate ProfessorYong Loo Lin School of MedicineNUS Graduate School for Integrative Science and EngineeringDepartment of BiochemistryNational University of Singapore8 Medical Drive, MD 7 #03-15Singapore 117597Tel: (65) 68747985Fax: (65) 67791453E-mail: [email protected]
Protein structure and functionPart - I
![Page 2: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/2.jpg)
Peptide bond
Amino acid
C-terminus terminates by a carboxyl group
N-terminus terminates
by an amino group
A peptide: Phe-Ser-Glu-Lys (F-S-E-K)
From amino acids to protein:
![Page 3: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/3.jpg)
The Shape of proteins:
OccursSpontaneously
Native conformation
determined by different Levels of structure
![Page 4: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/4.jpg)
Tertiary structure overall three-dimensional form of a polypeptide chain, which is stabilized by multiple non-covalent interactions between side chains.
Primary structure The linear arrangement (sequence) of amino acids and the location of covalent (mostly disulfide) bonds within a polypeptide chain. Determined by the genetic code.
Secondary structure local folding of a polypeptide chain into regular structures including the helix, sheet, and U-shaped turns and loops.
Quaternary structure: The number and relative positions of the polypeptide chains in multisubunit proteins. Not all protein have a quaternary structure.
Four Levels of Structure Determine the Shape of Proteins
![Page 5: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/5.jpg)
Bovine Insulin: the first sequenced protein
• In 1953, Frederick Sanger determined the amino acid sequence of insulin, a protein hormone .
• This work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence.
• it demonstrated that insulin consists only of amino acids linked by peptide bonds between α-amino and α-carboxyl groups.
• the complete amino acid sequences of more than 100,000 proteins are now known.
• Each protein has a unique, precisely defined amino acid sequence.
Primary Structure of a protein: determined by the nucleotide sequence of its gene
![Page 6: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/6.jpg)
C-peptide
Human: Thr-Ser-IleCow: Ala-Ser-ValPig: Thr-Ser-Ile
Chiken: His-Asn-Thr
Pro-insulin protein
Insuline
+ C peptide
C-peptide
Pro-insulin is produced in the Pancreatic islet cells
Primary Structure
65/66 30/31
![Page 7: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/7.jpg)
Amino acid substitution in proteins from different species
Conservative Substitution of an amino acid by another amino acid of similar polarity (Val for Ile in position 10 of insulin)
Non conservativeSubstitution involving replacement of an amino acid by another of different polarity (sickle cell anemia, 6th position of hemoglobin replace from a glutamic acid to a valine induce precipitation of hemoglobin in red blood cells)
Invariant residues Amino acid found at the same position in different species(critical for for the sructure or function of the protein)
![Page 8: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/8.jpg)
Protein conformation: most of the proteins fold into only one stable conformation or native conformation
More than 50 amino acids becomes a protein
![Page 9: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/9.jpg)
SECONDARY STRUCTURE
• Stabilized by hydrogen bonds
• H- bonds are between –CO and –NH groups of peptide backbone
• H-bonds are either intra- or inter- molecular
• 3 types : a-helix, b-sheet and triple-helix
![Page 10: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/10.jpg)
What forces determine the structure?
• Primary structure - determined by covalent bonds
• Secondary, Tertiary, Quaternary structures - all determined by weak forces– Weak forces - H-bonds, ionic interactions, van
der Waals interactions, hydrophobic interactions
![Page 11: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/11.jpg)
![Page 12: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/12.jpg)
Non covalent interactions
involved in the shape of proteins
![Page 13: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/13.jpg)
Secondary structures:
Helix: helix conformation was discovered 50 years ago in keratine abundant in hair nails, and horns
Sheet: discovered within a year of the discovery of helix.Found in protein fibroin the major constituant of silk
![Page 14: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/14.jpg)
The helix: result from hydrogen bonding, does not involve the side chain of the amino acid
![Page 15: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/15.jpg)
sheet:result from hydrogen bonding, does not involve the side chain of the amino acid
![Page 16: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/16.jpg)
Two type of Sheet structures
An anti paralellel sheet
A paralellel sheet
![Page 17: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/17.jpg)
TRIPLE HELIX
• Limited to tropocollagen molecule• Sequence motif of –(Gly-X-Pro/Hypro)n-• 3 left-handed helices wound together to give a
right-handed superhelix• Stable superhelix : glycines located on the
central axis (small R group) of triple helix• One interchain H-bond for each triplet of aas –
between NH of Gly and CO of X (or Proline) in the adjacent chain
![Page 18: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/18.jpg)
Triple helix of Collagen
![Page 19: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/19.jpg)
NONREPETITIVE STRUCTURES
• Helices/-sheets: ~50% of regular 2ostructures of globular proteins
• Remaining : coil or loop conformation• Also quite regular, but difficult to
describe• Examples : reverse turns, -bends
(connect successive strands of antiparallel -sheets)
![Page 20: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/20.jpg)
The Beta Turn(aka beta bend, tight turn)
• allows the peptide chain to reverse direction
• carbonyl O of one residue is H-bonded to the amide proton of a residue three residues away
• proline and glycine are prevalent in beta turns (?)
![Page 21: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/21.jpg)
-bulge• A strand of polypeptide in a -sheet may contain an “extra” residue
• This extra residue is not hydrogen bonded to a neighbouring strand
• This is known as a -bulge.
![Page 22: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/22.jpg)
The secondary structure of a telephone cord
A telephone cord, specifically the coil of a telephone cord, can be used as an analogy to the alpha helix secondary structure of a protein.
The tertiary structure of a telephone cord
The tertiary structure of a protein refers to the way the secondary structure folds back upon itself or twists around to form a three-dimensional structure. The secondary coil structure is still there, but the tertiary tangle has been superimposed on it.
Tertiary structure: the overall shape of a protein
or a telephone cord!!!
![Page 23: Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine](https://reader035.vdocuments.mx/reader035/viewer/2022062222/56814d60550346895dbaa6a4/html5/thumbnails/23.jpg)
Tertiary structure: the overall shape of a protein
Full three dimensional organization of a protein
The three-dimensional structure of a protein
kinase