PROTEIN MODELING

study for scioly

What are the four levels in a protein structure

1. Primary, 2. Secondary, #. Tertiary, 4. Quarternary

Hydrophobic

Gly G · Ala A · Val V · Leu L · Ile I · Met M · Phe F · Trp W · Pro P

Hydrophilic

Ser S · Thr T · Asn N · Gln Q · Tyr Y

Acidic

Asp D · Glu E

Basic

Lys K · Arg R · His H

Cysteine

Cys C

Primary; 2 main

Covalent, Peptide bonds,

Secondary; 3 main

Backbone hydrogen bonds, alpha helixes & beta sheets, C=O-H—N only

Tertiary; 2 main

Side chain forces + disulfides

Quaternary;2 main

two or more chains assembled together, same properties as teritary; side chain forces+Disulfides

Where does the native fold sit; connects to (delta “G”<0)

It sits at the place where the lowest free energy is there, bottom of the tunnel.

Hydrophobic effect

: Burying non polar side chains releases ordered water and raises entropy of the solvent

Enthalpy (ΔH)

ionic attractions; pull the fold together(bad)

Entropy (ΔS)

Chain loses freedom when it folds water gains freedom when the nonpolar side chains get buried, (good)

Hydrophobic effect time line

Water molecules H-bond to eachother—Nonpolar side chain interupts it and the water forms a cage around it—- the nonpolar chain is buried into the protein core and the cages break free and water is free—- ((ΔG) negative

1. Covalent;Peptide bond · Disulfide

Strongest, a disulfide (S-S) staples 2 different folds together

2. Ionic: Salt bridge

(-) charge plus a (+) charge. lys/arg+Asp/glu. Strong, on the surface usually

3. Hydrogen Bonds

Backbone H-bonds build every helix and sheet; sidechains H bonds fine tune the fold; weak alone

4. Van Der Walls

Very weak, extremely numerous. Only matters when atoms pack tightly — which is exactly what the core

does.

Stability: what breaks a protein( list the 4)

1. Heat, 2. PH change. 3. Salt. 4. Detergent

Heat

Atoms shake harder until weak H bonds and Van Der Walls shake apart

pH change

adds or removes H bonds so acidic and basic lose their connections, salt bridges switch off

Detergent (Denaturation)

Soap-like molecules coat the greasy core, so burying it no longer

pays off. The hydrophobic driver is cancelled.

Folding goes wrong 3 steps

1. Proteins that prevent mis-folding do not alter the final shape; they only guide it

2. When a protein is misfolded its hydrophobic core is exposed, sticking together to form stacked beta sheets.

3. Misfolded proteins force normal proteins into the wrong shape; causes diseases

Amino acids and α-carbon; 4 groups?

All amino acids share a central α-carbon bonded to four groups.

Amino group (–NH₂) — the N-terminus end

· Carboxyl group (–COOH) — the C-terminus end

· Hydrogen (–H) — always there, always the same

· R group — the SIDE CHAIN — the only part that differs

Peptide bond formation: what does it also leave

The Carboxyl group interacts with the Amino group and makes a condensation effect releasing water. leaves a repeating N–Cα–C pattern for every backbone, making all backbones identical.

Hydrophobic, & Hydrophilic

Buried in the core. Pack together by van der Waals. 2. Surface or core. Make H-bonds with water and each other.

Acidic, basic, cysteine

1. Surface. Pair with basic residues to form salt bridges, 2. Surface. Attract acidic residues and bind negative ligands.. 3. Two Cys can form a covalent disulfide bridge.

What is PkA?

Below its pKa a group keeps its H⁺. Above its pKa it loses the H⁺. —- pKa is simply the pH at which half the copies have lost their proton.

Can charge change?

it can change depending on pH.Below its pKa a group keeps its H⁺. Above its pKa it loses the H⁺

Zwitterion

free amino acid carries BOTH charges at once: the amino group

is –NH₃⁺ and the carboxyl group is –COO⁻. Net charge zero, but not

neutral atoms. That double-charged form is called a zwitterion.

Histidine and its pKa

About 6.0, meaning it can gain or lose a proton whole protein is at work, this is the reason why many enzyme use it to shuttle H*.

Isoelectric Point(Pl)

The overall electric charge of an object, changes as pH changes.

Salt bridge IONIC

A + side chain meets a − one. Lys or Arg with Asp or Glu. Strongest of the non-covalent

options.

Hydrogen bond: POLAR

An –OH or –NH donates to an O or N. Ser, Thr, Tyr, Asn, Gln and His are the regulars.

Disulfide bridge; COVALENT

Two cysteines oxidize and bond S–S. A permanent staple — the only covalent

side-chain link.

Hydrophobic packing ENTROPIC

Nonpolar side chains press together in the core, excluding water. Held by van der Waals

once close.

Aromatic stacking VAN DER WAALS

Flat rings of Phe, Tyr and Trp stack like coins.

Common in cores and binding pockets.

"What are the 6 steps of influenza infection?

Attach → Enter → Acidify → Fuse → Copy → Escape."

"What does hemagglutinin (HA) do?

"Binds sialic acid on host cells.

"What does neuraminidase (NA) do

"Cuts sialic acid so new viruses can escape

How does influenza enter a cell?

Endocytosis: the cell takes the virus into an endosome

What does low pH do to HA

Changes its shape to trigger membrane fusion.

What does HA2 do?

Its fusion peptide helps viral and host membranes merge

What happens during viral copying?

Viral RNA is released and used to make new virus parts

What is innate immunity?"

Fast, general defense; includes interferon, macrophages, and NK cells."

"What does interferon do?

Warns nearby cells to activate antiviral defenses

What do macrophages and NK cells do

Macrophages engulf pathogens; NK cells kill infected cells

What is adaptive immunity?

"Specific defense involving B cells, antibodies, T cells, and memory cells

What do B cells do?

Make antibodies that bind HA and block infection

What do T cells do?

"Kill infected cells

"What do memory cells do

Help the immune system respond faster upon re-exposure."

What is antigenic drift?

"Small mutations change viral antigens; causes seasonal changes

What is antigenic shift

Major change from reassortment of influenza RNA segments; can cause pandemics."

What is HA?

"Influenza surface protein that binds host receptors and helps fusion

"What are HA1 and HA2?

"HA1 = receptor-binding head; HA2 = fusion stalk.

What is HA0?

Uncut HA precursor; host proteases cut it into HA1 and HA2.

What are the three parts of the HA binding site?

130-loop, 190-helix, and 220-loop; Put this in your cheat sheet instead.

What receptor linkage does avian influenza usually prefer?

α2-3-linked sialic acid.

What receptor linkage does human-adapted influenza usually prefer?

α2-6-linked sialic acid.

What is the key role of Gln226?

Associated with human-type α2-6 receptor preference in the studied HA.

What is the key role of Leu226?

Associated with avian-type α2-3 receptor preference in the studied HA.

Which other HA residues help receptor binding?

Asp190 and Asp225; put detailed residue positions in your cheat sheet.

What is a disulfide bridge?

A covalent S–S bond between two cysteine residues.

What amino acid can gain or lose a proton near body pH?

Histidine; useful in enzyme catalysis.

What does the HA structure look like?

A trimer structure consisting of a globular head (HA1) and a stem/stalk region (HA2); Search up a picture of this online and add it to the card.

What are the 3 main secondary structures?

Alpha helix, beta sheet, and loop/turn.

What does an alpha helix look like?

A coiled spring shape; Search up a picture of this online and add it to the card.

What holds an alpha helix together?

Backbone hydrogen bonds between residues n and n+4.

What does a beta sheet look like?

Flat arrows held together by hydrogen bonds; Search up a picture of this online and add it to the card.

What do arrows in beta sheets show?

The N-to-C direction of each strand.

What is the difference between parallel and antiparallel sheets?

Parallel strands run the same way; antiparallel strands run opposite ways.

What is a loop or turn?

An irregular segment connecting helices and sheets.

Which amino acids favor helices?

Ala, Leu, Met, Glu, Gln.

Which amino acids favor sheets?

Val, Ile, Thr, Tyr, Trp, Phe.

Which amino acids are common in turns?

Gly and Pro; Gly is flexible, Pro creates bends.

What is a 3₁₀ helix?

A tighter helix with 3 residues per turn and n-to-n+3 hydrogen bonds.

What is a pi helix?

A wider, rare helix with n-to-n+5 hydrogen bonds.

What is a Ramachandran plot?

Shows allowed protein backbone phi (φ) and psi (ψ) angles.

Where are alpha helices and beta sheets on a Ramachandran plot?

Alpha helices: bottom-left; beta sheets: upper-left.

How does Gly differ from Pro on a Ramachandran plot?

Gly is highly flexible with many allowed regions; Pro is highly restricted; Search up a picture of this online and add it to the card.

What is a protein motif?

A recurring arrangement of secondary structures.

What is a beta-hairpin?

Two antiparallel strands joined by a turn.

What is a Greek key?

Four antiparallel strands folded into a distinctive pattern.

What is a beta-barrel?

A beta sheet rolled into a closed barrel.

What is a coiled coil?

Two or more alpha helices wrapped around each other.

What is a beta-alpha-beta motif?

Two parallel beta strands connected by an alpha helix.

What is the protein structural hierarchy?

Secondary structure → motif → domain → tertiary structure.

What should you ask about a residue in a protein structure?

Is it buried or exposed, and what does it touch?

Which residues are usually buried?

Nonpolar residues such as Leu, Ile, Val, Phe, and Met.

Which residues are usually exposed?

Polar or charged residues such as Lys, Arg, Asp, Glu, Ser, and Asn.

What is a salt bridge?

Attraction between oppositely charged side chains.

What is a hydrogen-bond network?

Several groups connected by hydrogen bonds.

What is a hydrophobic cluster?

Nonpolar side chains packed away from water.

What is a disulfide bond?

A covalent S–S bond between two cysteines.

What distances should you memorize for protein interactions?

Hydrogen bonds are typically 2.7 to 3.3 Å; salt bridges are under 4 Å; van der Waals are 3.3 to 4.0 Å; Put this in your cheat sheet instead.

What is a ligand?

A molecule that binds to a protein.

How do you answer a ligand-interaction question?

Name the residue, interaction type, and what it contributes.

What do Trp153 and Leu194 do in the HA binding pocket?

Help form its hydrophobic surface.

What do His183 and Thr136 do in the HA binding pocket?

Form hydrogen bonds with sialic acid.