Protein Biophysics

Amino Acids

building blocks of proteins.

carboxylic group and an amino group on the alpha solution

Amino Acids Contain

side group

Amino acids contain different

Structural

Collagen and Keratin

Contractile

Actin and Myosin

Transport

Hemoglobin and Lipoproteins

Storage

Casein and Ferritin

Hormone

Insulin and Growth

Enzyme

Sucrase and Trypsin

Protection

Immunoglobulins

Glycine and Alanine

Examples of Amino Acids

nonpolar

with hydrocarbon side chains.

polar

with ionic side chains.

acidic

(-COOH) side chains.

basic

with -NH2 side chains.

Nonpolar Amino Acids

when the R group is H, alkyl, or aromatic.

Polar Amino Acids

when the R group is an alcohol, thiol, or amide.

carboxylic acid

An amino acid is acidic when the R group is

amine

An amino acid is basic when the R group is

Glycine

Which amino acid is not chiral

stereoisomers

Amino Acids have Fischer projections that are

Peptide Bond

• is an amide bond

• forms between the carboxyl group of one amino acid and the amino group of the next amino acid.

Primary Structure

• particular sequence of amino acids.

• backbone of a peptide chain or protein. linear.

Secondary Structure

Alpha Helix is a

secondary structure of an alpha helix

• 3D spatial arrangement of amino acids in a polypeptide chain.

• corkscrew shape that looks like a coiled “telephone cord”.

Secondary Structure

Beta Pleated Sheet

secondary structure of a beta pleated sheet

• consists of polypeptide chains arranged side by side.

• has hydrogen bonds between chains.

• has R groups above and below the sheet.

• typical of fibrous proteins such as silk.

Tertiary Structure

• overall three-dimensional shape.

• determined by attractions and repulsions between the side chains of the amino acids in a peptide chain.

Functional Importance of Tertiary Structure

A. Shape determines the function

B. Misfolding of the tertiary structure can lead to loss of function or diseases

Quaternary Structure

• combination of two or more protein units.

• stabilized by the same interactions found in tertiary structures.

• of hemoglobin consists of four polypeptide chains as subunits.

Enzymes

• Catalyze nearly all the chemical reactions taking place in the cells of the body.

• Increase the rate of reaction by lowering the energy of activation.

active site

In an enzyme-catalyzed reaction, a substrate attaches to the

Enzyme-substrate complex

What forms in an enzyme-catalyzed reaction

Optimum pH

Contains R groups of amino acids with proper charges at

37 deg.C

optimum temperature for humans

low temperature

Enzymes show little activity at

high temperatures

enzyme loses activity at

rate of reaction

As substrate concentration increases, this also increases

Zwitterion

Ionization of amine and carboxyl group

Salt bridge/ion pair

Ionization of Amino Acid Side chain between two oppositely charged group results is a

Ionic Bonds

Results from electrostatic attractions between positively and negatively charged side chains of amino acids

Hydrogen bond

weak, noncovalent attraction

Hydrogen bond

occurs when A hydrogen atom is covalently bonded to an electronegative atom like oxygen (O) or nitrogen (N).

Secondary: stabilizes a-helices and b-sheets

Tertiary: stabilize folding by linking polar side chains

Quaternary: Help align and hold multiple subunits together

Importance of Hydrogen bonds in protein structure

Disulfide Linkages

formed between the thiol groups of two cysteine residues by the process of oxidative folding

Dispersion forces

arise when a normally nonpolar atom becomes momentarily polar due to unequal distribution of electrons, leading to instantaneous dipole that induces shift of electrons in a neighboring nonpolar atom.

Dipole-induced interactions

When a nonpolar molecule approaches a polar molecule (with a permanent dipole), a dipole will be induced in the nonpolar molecule.

London Dispersion

exist among all molecules and contributes to the overall Van der Waals’ forces.

Fibroin

major protein in silk, in which a high proportion of amino acids in the protein have nonpolar side chains. 

Hydrophobic Effect

Water molecules form a cage-like structure (clathrates) around the nonpolar molecule.  Because nonpolar groups cannot engage in hydrogen bonding, the protein folds in such a way that these groups are buried in the interior part of the protein structure, minimizing their contact with water.

(a) ionic bonding

(b) hydrogen bonding

(c) disulfide linkages 

(d) dispersion forces

Four interactions stabilize the tertiary structure of a protein:

Denaturation

disruption of bonds in the secondary, tertiary and quaternary protein structures; loss of a protein’s native structure.

Heat and Organic Compounds

During denaturation, this break apart H bonds and disrupt hydrophobic interactions.

Acids and Bases

During denaturation, this break H bonds between polar R groups and disrupt ionic bonds

heavy metal ions

During denaturation, this reacts with S-S bonds to form solids.

Agitation

During denaturation, whipping that stretches peptide chains until bonds break.

Prion

• misfolded protein that becomes infectious

Variant Creutzfeldt-Jakob Disease (vCJD)

What disease can you get from misfolded protein

Torsion Angles

Angles between two planes and involves 4 consecutive atoms in structural biology

carbonyl

In the analysis of polypeptide backbone bond angles, this group has a partial negative charge

amide nitrogen

In the analysis of polypeptide backbone bond angles, this has a  partial positive charge, which set up a small electric dipole.

peptide C-N bond

has a partial double-bond character (partial sharing of two pairs of electrons between O and N

Torsion Angles

defines rotation about a bond

4

how many atoms are needed to define the torsion angle about B-C bond

Backbone

it has a repeating motif of -N, - Ca and - C’

Omega

• C′-N (peptide bond)

• Defined by C_ɑ  - Cʹ - N - C_ɑ

Φ (phi)

• N - C_ɑ

• Defined by Cʹ - N - C_ɑ  - Cʹ

𝛹 (psi)

• C_ɑ  - Cʹ

• Defined by -N - C_ɑ -Cʹ - N

-180° and +180°

in principle, Φ and 𝛹  can have any value between

angle of rotation = φ

Between the amide nitrogen and the a-carbon

Angle of rotation = ψ

Between the a-carbon and the carbonyl carbon

no rotation = ⍵)

Between the carbonyl carbon and the amide nitrogen

Glycine

an amino acid with hydrogen as its R group, hence, it is quite sterically unhindered. Therefore, glycine is found in loops/turns in the protein tertiary structure.

Ramachandran plot

The φ/ψ plot of the amino acid residues in a peptide

Ramachandran plot

way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure

the white areas

In the ramachandran plot, it  correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radi

Glycine

lacks side chains

Alpha helix, Beta sheet and Collagen triple helix

Types of Secondary Structure

Alpha helix

• Right handed (clockwise) and left handed (counterclockwise)

• Most are right-handed

Beta sheet

• Parallel and Anti-parallel

• Antiparallel are more stable

Collagen Triple Helix

• Three left-handed chains are super twisted about each other to form a right-handed triple helix

• Opposite direction of coiling resists unwinding

• Held by hydrogen bonds