proteins: function & structure
DESCRIPTION
Proteins: Function & Structure. Proteins. Cellular Overview Functions Key Properties Core Topics Amino Acids: properties, classifications, pI Primary Structure, Secondary Structure, and Motifs Tertiary Structure Fibrous vs. Globular Quaternary Structure. Amazing Proteins: Function. - PowerPoint PPT PresentationTRANSCRIPT
Proteins: Function & Structure
Proteins1. Cellular Overview
1. Functions2. Key Properties
2. Core Topics1. Amino Acids: properties, classifications,
pI
2. Primary Structure, Secondary Structure, and Motifs
3. Tertiary Structure1. Fibrous vs. Globular
4. Quaternary Structure
Amazing Proteins: Function1. Catalysts (Enzymes)
2. Transport & Storage
• The largest class of proteins, accelerate rates of reactions
DNA Polymerase
Hemoglobin
Catalase CK2 Kinase
Ovalbumin CaseinSerum albumin Ion channels
Amazing Proteins: Function4. Structural
5. Generate MovementCollagen Keratin Silk Fibroin
Actin Myosin
Amazing Proteins: Function5. Regulation of Metabolism and Gene
Expression
6. Protection
Insulin Lac repressor
Immunoglobulins Thrombin and Fibrinogen
RicinVenom Proteins
Amazing Proteins: Function7. Signaling and response (inter and
intracellular)
Apoptosis
Membrane proteinsSignal transduction
Amazing Proteins: Properties•Biopolymers of amino
acids•Contains a wide range
of functional groups•Can interact with
other proteins or other biological macromolecules to form complex assemblies
•Some are rigid while others display limited flexibility
a-Amino Acids: Protein Building Blocks
C
O
C
R
H O-
NH3+
Carboxyl group
R-group or side-chain
a-amino group
a-carbon
Amino acids are zwitterionic•“Zwitter” = “hybrid” in German
•Fully protonated forms will have specific pKa’s for the different ionizable protons
•Amino acids are amphoteric (both acid and base)
C
O
C
R1
H OH
NH2 C
O
C
R1
H O-
NH3+
C
O
C
R1
H O-
NH3+
Stereochemistry of amino acids
•AA’s synthesized in the lab are racemic mixtures. AA’s from nature are “L” isomers
•These are all optically-active except for glycine (why?)
Stereochemistry of amino acids (AA)
Synthesis of Proteins
C
O
C
R1
H O-
NH3+
C
O
C
R1
H
NH3+
C
O
C
R2
H O-
NH
C
O
C
R2
H O-
NH3++
peptide bond
+ H2O
Synthesis of Proteins
+ C
O
C
R3
H O-
NH3+
C
O
C
R1
H
NH3+
C
O
C
R2
H O-
NH
C
O
C
R1
H
NH3+
C
O
C
R2
H
NHC
O
C
R3
H O-
NH
Synthesis of Proteins
C
O
C
R1
H
NH3+
C
O
C
R2
H
NHC
O
C
R3
H O-
NH + C
O
C
R4
H O-
NH3+
C
O
C
R1
H
NH3+
C
O
C
R2
H
NHC
O
C
R3
H
NH
C
O
C
R4
H O-
NHN-Terminal End
C-Terminal End
Synthesis of Proteins
C
O
C
R1
H
NH3+
C
O
C
R2
H
NH C
O
C
R3
H
NH C
O
C
R4
H O-
NH
C
O
C
R4
H
NH3+
C
O
C
R2
H
NH C
O
C
R3
H
NH C
O
C
R1
H O-
NH
=≠
Synthesis of Proteins
C
O
C
R1
H
NH3+
C
O
C
R2
H
NH C
O
C
R3
H
NH C
O
C
R4
H O-
NH
=≠
C
O
C
R1
H
NH3+
C
O
C
R3
H
NH C
O
C
R2
H
NH C
O
C
R4
H O-
NH
Synthesis of Proteins
C
O
C
R1
H
NH3+
C
O
C
R2
H
NH C
O
C
R3
H
NH C
O
C
R4
H O-
NH
≠
C
O
C
R1
H
NH3+
C
O
C
R3
H
NH C
O
C
R2
H
NH C
O
C
R4
H O-
NH
C
O
C
R4
H
NH3+
C
O
C
R2
H
NH C
O
C
R3
H
NH C
O
C
R1
H O-
NH
≠
COMMON AMINO ACIDS20 common amino acids make up the multitude of proteins we know of
Amino Acids With Aliphatic Side Chains
Amino Acids With Aliphatic Side Chains
Amino Acids With Aliphatic Side Chains
Amino Acids With Aromatic Side Chains
Amino Acids with Aromatic Side Chains Can Be Analyzed by UV Spectroscopy
Amino Acids With Hydroxyl Side Chains
Amino Acid with a Sulfhydryl Side Chain
Disulfide Bond Formation
Amino Acids With Basic Side Chains
Amino Acids With Acidic Side Chains and Their Amide Derivatives
There are some important uncommon amino acids
pH and Amino Acids
Net charge: +1 Net charge: 0 Net charge: -1
Characteristics of Acidic and Basic Amino Acids
•Basic amino acids▫High pKa ▫Function as bases
at physiological pH
▫Side chains with N
•Acidic amino acids▫Low pKa ▫Negatively
charged at physiological pH
▫Side chains with –COOH
▫Predominantly in unprotonated form
Isoelectic point (pI)
•the pH at which the compound is electrically neutral▫Equal number of (+) and (-) charge
•At pH < pI amino acid is (+)•At pH > pI amino acid is (-)
•CRITICAL FOR: protein analysis, purification, isolation, crystallization
Protein StructureWe use different “levels” to fully describe the structure
of a protein.
Primary Structure•Amino acid sequence•Standard: Left to Right means N to C-
terminal
•Eg. Insulin (AAA40590)
•The info needed for further folding is contained in the 1o structure.
MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLEAGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP
Secondary Structure•The regular local structure based on the
hydrogen bonding pattern of the polypeptide backbone▫α helices▫β strands (β sheets)▫Turns and Loops
•WHY will there be localized folding and twisting? Are all conformations possible?
Consequences of the Amide PlaneTwo degrees of freedom per residue for the
peptide chain •Angle about the C(alpha)-N bond is
denoted phi •Angle about the C(alpha)-C bond is
denoted psi •The entire path of the peptide backbone is
known if all phi and psi angles are specified
•Some values of phi and psi are more likely than others.
The angles phi and psi are shown here
See blackboard for explanation why the peptide bond is planar
Unfavorable orbital overlap precludes some combinations of phi and psi
•phi = 0, psi = 180 is unfavorable •phi = 180, psi = 0 is unfavorable •phi = 0, psi = 0 is unfavorable
Sasisekharan
Steric Constraints on phi & psi
•G. N. Ramachandran was the first to demonstrate the convenience of plotting phi,psi combinations from known protein structures
•The sterically favorable combinations are the basis for preferred secondary structures
α Helix
• First proposed by Linus Pauling and Robert Corey in 1951.• 3.6 residues per turn, 1.5 Angstroms rise per residue• Residues face outward
α Helix
•α-helix is stabilized by H-bonding between CO and NH groups
•Except for amino acid residues at the end of the α-helix, all main chain CO and NH are H-bonded
α Helix representation
β strand
•Fully extended•β sheets are formed by linking 2 or more
strands by H-bonding
• Beta-sheet also proposed by Corey and Pauling in 1951.
PARALLEL
ANTIPARALLEL
The Beta Turn(aka beta bend, tight turn) • allows the peptide chain to reverse
direction • carbonyl C of one residue is H-bonded
to the amide proton of a residue three residues away
• proline and glycine are prevalent in beta turns
Mixed β Sheets
Twisted β Sheets
Loops
What Determines the Secondary Structure?
•The amino acid sequence determines the secondary structure
•The α helix can be regarded as the default conformation – Amino acids that favor α helices:
Glu, Gln, Met, Ala, Leu – Amino acids that disrupt α helices:
Val, Thr, Ile, Ser, Asx, Pro
What Determines the Secondary Structure?
•Branching at the β-carbon, such as in valine, destabilizes the α helix because of steric interactions
•Ser, Asp, and Asn tend to disrupt α helices because their side chains compete for H-bonding with the main chain amide NH and carbonyl
•Proline tends to disrupt both α helices and β sheets
•Glycine readily fits in all structures thus it does not favor α helices in particular
Can the Secondary Structure Be Predicted?•Predictions of secondary structure of
proteins adopted by a sequence of six or fewer residues have proved to be 60 to 70% accurate
•Many protein chemists have tried to predict structure based on sequence ▫Chou-Fasman: each amino acid is assigned a
"propensity" for forming helices or sheets ▫Chou-Fasman is only modestly successful and
doesn't predict how sheets and helices arrange ▫George Rose may be much closer to solving the
problem. See Proteins 22, 81-99 (1995)
Modeling protein folding with Linus (George Rose)
Tertiary Structure•The overall 3-D fold of the polypeptide
chain •The amino acid sequence determines the
tertiary structure (Christian Anfinsen)•The polypeptide chain folds so that its
hydrophobic side chains are buried and its polar charged chains are on the surface▫Exception : membrane proteins▫Reverse : hydrophobic out, hydrophilic in
•A single polypeptide chain may have several folding domains
•Stabilized by H-bonding, LDF, noncovalent interactions, dipole interactions, ionic interactions, disulfide bonds
Fibrous and Globular Proteins
Fibrous Proteins•Much or most of the polypeptide chain is organized approximately parallel to a single axis
•Fibrous proteins are often mechanically strong
•Fibrous proteins are usually insoluble
•Usually play a structural role in nature
Examples of Fibrous Proteins•Alpha Keratin: hair, nails, claws, horns,
beaks
•Beta Keratin: silk fibers (alternating Gly-Ala-Ser)
Examples of Fibrous Proteins•Collagen: connective
tissue- tendons, cartilage, bones, teeth▫Nearly one residue out
of three is Gly ▫Proline content is
unusually high ▫Unusual amino acids
found: (4-hydroxyproline, 3-hydroxyproline , 5-hydroxylysine)
▫Special uncommon triple helix!
Globular Proteins•Most polar residues face the outside of
the protein and interact with solvent •Most hydrophobic residues face the
interior of the protein and interact with each other
•Packing of residues is close but empty spaces exist in the form of small cavities
•Helices and sheets often pack in layers •Hydrophobic residues are sandwiched
between the layers •Outside layers are covered with mostly
polar residues that interact favorably with solvent
An amphiphilic helix in flavodoxin:
A nonpolar helix in citrate synthase:
A polar helix in calmodulin:
Quaternary Structures•Spatial arrangement of subunits and the
nature of their interactions. Can be hetero and/or homosubunits
•Simplest example: dimer (e.g. insulin)
ADVANTAGES of 4o Structures▫ Stability: reduction of surface to volume ratio ▫ Genetic economy and efficiency ▫ Bringing catalytic sites together ▫ Cooperativity
Protein Folding• The largest
favorable contribution to folding is the entropy term for the interaction of nonpolar residues with the solvent
•CHAPERONES assist protein folding▫ to protect nascent
proteins from the concentrated protein matrix in the cell and perhaps to accelerate slow steps