pI Example calculation- Arginine
Ionizable group (HA) pKa
H H3N C COOH H2N COO+
2 ~2
7
9.5 12.5
-carboxyl (-COO-) -amino (-H3N+)
((NHR)2C=NH2+)
- + +
+ +
+ +
0 +
pI value will be half-way between pH 9.5 and pH 12.5 = 11
1
~9.5
Guanidinyl 12.5
TOTAL CHARGE: +1 (at each pH)
+1 + -
=
pH
(CH2)3-NH-C-NH2 NH2+
Protein: Secondary and Tertiary Structure
Jan. 15, 2008
2
Review
Amino acid derivatives -aminobutyric acid, dopamine: neurotransmitters Histamine: local mediator of immunological response Uncommon amino acids Ornithine, citrulline: Arg biosynthesis and urea metabolism Thyroxine: thyroid hormone Azaserine: fungi toxin that is used in medicine as an antibiotic S-adenosylmethionine: methylating reagent Homocysteine: intermediate in amino acid metabolism -cyanoalanine: cyanide metabolism metabolite in plants and E. coli
3
Review
Phi () and Psi () torsional angles Ramchandran plot shows regions where there are no steric conflicts Primary structure: the aa sequence of a polypeptide chain Secondary structure: local spatial arrangement of a polypeptide's backbone atoms
4
New Material
Cystine bonds play a structural role in proteins Protein primary structure similarity across species More in depth on fibrous and globular proteins More on protein secondary structure Intro to protein tertiary structure
5
Structure of cystine, a disulfide bond
6
Bovine pancreatic ribonuclease A contains 124 amino acid residues. Four intramolecular disulfide bridges (SS) form crosslinks in this polypeptide These disulfides are depicted by yellow bars.
7
What can the primary structure tell us?
Primary structure helps us predict the function of a protein Homologous proteins from different organisms have homologous sequences Evolutionary relatedness can be inferred from sequence homology e.g., cytochrome c is highly conserved
8
Amino Acid Sequences of Cytochromes c from 38 Species.
9
Two Major Classes of Proteins
Fibrous: this class of proteins are elongated molecules w/ welldefined secondary structures and function primarily in a structural role, i.e. they hold things together.
- and -keratins, silk fibroin, collagen, elastin
Globular: most of the chemical work is done by this class of protein named so because of their compact 3-D fold.
Synthesizing, transporting, metabolizing, catalyzing,etc.
10
Secondary Structure
Linus Pauling studied the crystal structures of the 20 amino acids, postulated 4 principles that a polypeptide structure should obey:
Conserved bond lengths and angles with those of the free amino acids No two atoms should approach closer than their van der Waals radii would allow Amide group must remain planar & in the trans configuration Some kind of non-covalent bonding is necessary to stabilize a regular folding. The most obvious possibility being the Hbond between amide protons and carbonyl oxygens
In the end, he came up with two possible structures: the -helix and the -sheet.
11
Secondary Structure
12
-strand
N
C
13
Beta-sheets
A beta-sheet refers to two or more betastrands held together by interchain H-bonds If strands are both oriented in the same direction the sheet is called a parallel betasheet If strands are oriented opposite to each other, the sheet is called an anti-parallel beta sheet
14
Parallel pleated sheet
15
Antiparallel Pleated Sheet
16
Fibroin: silk protein
Rich in Ala and Gly that interdigitate (interweave)
17
Nonrepetitive Secondary Structures Example: Reverse turns ( turns) in polypeptide chains
18
Connections between adjacent polypeptide strands in pleated sheets.
Page 229
19
Let's talk about helices some more
20
Helices in general
Can be L or R handed Helix itself has a dipole moment
Amino end is partially positive Carboxyl end is partially negative
-
+
There are other kinds of helices that can differ in the number of residues per turn, but the geom. of an alphahelix is most favorable
21
Review of alpha-helix
Right-handed when made of L-amino acids By definition 3.6 residues per turn Intrachain H-bonds are formed between peptide bond elements 4 residues apart All H-bonds in alpha-helix are oriented along its axis; R-groups are oriented away from the axis Common in fibrous and globular proteins -
+
22
Where can we find alphahelices?
keratin
Mammals In hair: keratin dimers form L-handed twists It's structure is primarily stabilized by Cys (about 30%)
keratin
Reptiles, birds Stronger than -keratin
23