protein structure and function

Proteins are typically described as N-terminus (free amino terminus) to C-terminal. This is also the direction of synthesis on the ribosome.


**Another aspect of protein structure is whether they are transmembrane. Proteins, with the help of intracellular machinery, can insert hydrophobic regions into the membrane with parts of the protein protruding into the luminal and cytosolic spaces.

Amino acids are conjoined through peptide bonds. Peptide bonds are amide bonds (bonds between a carboxylate group and an amine).Peptide bonds do not rotate along the C-N bond because they have partial double bond characteristics. Therefore, 6 atoms lie within a plane: the carbonyl oxygen, the alpha-carbon (central carbon of the amino acid), the carbonyl carbon)

Sequence of amino acid and any modifications made to them

Folding proteins helps acquire a certain structure (alpha helices, beta sheets, turns and bends)

Arises from wanting to satisfy Hydrogens Bonds on the main chain carboxyl groups and amide groups

H bonds + or – 1 kcal/mol per bond to the stability of the secondary structure element. Alpha-helices and beta-sheets are often connected via turns as linkers, and can occur in many patters (eg, helix-turn-helix).

Alpha-helices and beta-sheets, tend to maximize the hydrogen bonding in the core of the protein. The regular repeat structures form hydrogen bonds for all the available backbone amide carbonyl and nitrogen groups

Organization of secondary structures into a domain – only a single peptide

Domain structures are held in place through hydrophobic interactions, disulfide bonds, ionic bonds (rare), and sometimes hydrogen

bonds.

a cost in stability of ~ +7 kcal/mol, unless it can interact with water instead. So, failing to satisfy H-bonding is destabilizing. So, the protein will optimize (make huge use of) Hbonding in a manner consistent with the secondary structures to the extent possible. The side chains, R-groups, determine what kind of secondary structure is favored.  Some proteins have all these secondary structures, while other proteins have predominately one kind of secondary structure.

Several peptides into a functional protein that incorporates second and tert into assembly (ex hemoglobin)

UAA

UAG

UGA

AUG MET

Is a RNA molecule that catalyzes and chemical reaction (ex peptidyl transferase in polypep chain formation)

AA in the ribosome are attached to their tRNAs by an ester bond (R’CO - O - R) between the carboxyl terminus and  either the 2’ or 3’ OH groups of the ribose sugar of an adenosinethe ester bond in the (P)eptidyl  site is cleaved, and peptidyl transferase catalyzes a condensation  reaction between its carboxyl terminus and the amino terminus of  the amino acid in the (A)mino site

Central alpha carbon atom

Amino group

CA group

hydrogen

R group (side chain)

4 diff groups connected to tetrahedral alpha carbon atom

**mirror images  = L isomer and D isomer (only L in proteins)

Charge

Hydrophobicity

Polarity

Aromaticity

Size

**some AA have specific effects on secondary structure (Pro Gly)

**chemical reactivity associated with diff groups is essential function of enzymes

The proteins that catalyze specific chemical reactions

GLY Glycine:

Form twisted helices with other pro

Very flexible backbone

Smallest AA R group (allows tight packing of strands to form helix

Often found in turns and active sites



ALA Alanine:

Single methyl group

Moderately hydrophobic

PRO Proline:

Breaks or kinks α-helices in secondary structure

Specialized structures

Major constituent of collagen

Modified (hydroxylated)

VAL Valine

LEU Leucine

ILE Isoleucine

Hydrophobic and found in cores of proteins

When a muscle protein breaks to AA, the amino group of BCAA is sent to pyruvate to make alanine and the carbons are sent to TCA to extra E for the muscles

SER Serine: hydroxyl groups are very reactive and can be phosphorylated or  glycosylated easily.

THR Threonine: **same as above** participate in active sites to carry out covalent chemistry or acid/base chemistry                                                                           

CYS Cysteine: form a “disulfide” bond with another cysteine, oxi rxn, red is reverse. critical in protein tertiary structure formation and sometimes in quaternary structure.

** cys-SH + cys-SH > cys-S-S-cys + 2H   (note – the Hydrogens are incorporated into other molecules). • Reducing agents specific for disulfides can reverse this, such as glutathione, which is part of the intracellular redox system.

MET Methionine: methyl is attached to sulfur of methionine to give molecules that need 1 carbon group to grow larger

PHE Phenylalanine: can be converted to tyrosine by hrdoxylation rxn

TYR Tyrosine: precursor for other compounds, is phosphorylated during growth factor receptor activation, is a docking site for proteins with SH2 domain

TRP Tryptophan: **can be converted to B vitamin, niacin

Somewhat hydrophobic, large

Stabilize binding of aromatic rings (ex ATP)

Stacking interaction with substrates

Tyrosine phosphorylation (is the addition of a phosphate (PO43−) group to the amino acidtyrosine on a protein)

Active sites

ASN Aspartate

GLN Glutamate

On the exterior to impact solubility

In active sites

Protein modifications

ASP Asparagine (or aspartic acid)

GLU Glutamine (or glutamic acid)

Polar

Can be reactive

Asparagine is the site of N-linked glycosylation

LYS Lysine: undergoes modifications

ARG Arginine: part of urea cycle

HIS Histidine: often in active sites, pKis near neutral and can be readily protonated, can bind or release protons (act as buffer(mechanism that keep the pH in the optimal required range all the time)) near physio PH

Charged at neutral PH

Typically found on the exterior to render the protein soluble

Valine, Leucine, isoleucine, methionine, alanine

Provide hydrophobicity

Structure

Important in folding

Serine, threonine, tyrosine

Can be phosphorylated – critical in signaling

Can be glycosylated, important for many functionals and structural aspects of proteins

Important in many enzymatic reactions.

Tyrosine, phenylalanine, tryptophan (histidine also has aromatic ring properties)

Structural, hydrophobic

Often found in binding sites, stabilize other aromatic ring systems

Glutamate and Aspartate

Imparts charge

Lysine, Arginine, Histidine

Impart charge

Participate in enzymatic reactions.

Cysteine

Can form disulfide bonds – critical for tertiary structure and sometimes quaternary structure.

Similar to serine; also participates in enzymatic chemistry.

describes the relation of pH  to the acid and conjugate base forms of a titratable group, in  biological systems.

The equation can be used to do the following: Estimate the pH of a buffer solution

Find the equilibrium pH in acid-base reactions Calculate the isoelectric point of proteins pKa  is the pH where the acid and conjugate base forms of a compound are equal in concentration.  The pKa is the best buffering point of a pH buffer.

pKa values of the side chain define  and important pKa residues name and pKa

determine the overall charge and solubility of a protein.

A: asp 3.9 glu 4.3

B: lys 10.5 arg 12.5 his 6.0

Cysterine: cys 8.3

pKa is the best buffering point of PH buffer

pI, is the pH value where the molecule is net neutral (net charge is zero).

pH that proteins are net neutral at often makes them less soluble, and they may precipitate out of solution.

** Most proteins (but by no means all), are more acidic, meaning that they have a pI of less than 7; typical values are 5-6. However, the pI values can range up**

The overall charge of a polypeptide/protein is the sum total of all the +and charges on the side chains of the amino acids constituting the protein

** N-terminus is always a +1 at pH 7.4 and the C-terminus is always a -1 atpH 7.4, unless they are modified

** One exception is histidine.  Side chain pKa is 6, so it should be deprotonated most of the time, often times near the surface of the proteins, the local effect chane the pKa enough that it is charged.  Some will count a His as a + 0.5 charge

CA: two angles of rotation associated with each Amino acid: N-Cα (alpha C on N of AA) and Cα-CO (Carbonyl oxy and C, the alpha C). These are restricted by the R groups

NH: amide bond has double-bond character, and does not rotate: This is a key aspect of higher order structure. Is planar, planarity is of 6 atoms (key characteristic of pro structure)

right-hand helices stabilized by H-bonds running roughly parallel to the helix axis, require H bonding to residues nearby in the sequence (4 AA distant)

Certain amino acids preferentially form α-helices

The R-groups, side chains, all point out from the helix

α-helices satisfy all backbone (main chain) Hydrogen bonds.

is a rod-like structure with the  peptide chain tightly coiled and the side chains  of amino acid residues extending outward from  the axis of the spiral

**hemoglobin (soluble, quaternary structure 2a globin 2b globin, affect one another to cause release or binding of oxygen) and rhodopsin (transmembrane protein) are 2 alpha helical proteins

Each carbonyl group is hydrogen-bonded to the amide-hydrogen of a peptide bond that is four residues away along the same chain

There are 3.6 amino acids per turn

The helix winds as a right-handed screw.

β-sheets form flat sideby-side planes of amino acids and is extended which implies H bond interactions can occur among residues that are distant in primary sequence

The R-groups point up and down (alternating) from the plane of the sheet

All main chain hydrogen bonds are satisfied, except edges

**porin (transmembrane protein form beta barrels in soluble proteins) & IgI (held together by disulfide bonds into its quaternary structure all structures folded make Y shape)

It is pleated because the alpha-carbon-carbon bonds are  tetrahedral and cannot exist in a planar  configuration

This causes the structure to appear “pleated” viewed from the side

If the polypeptide chains runs in the same direction,  it forms a parallel β-sheet

If the polypeptide chains runs in opposite direction, they form an antiparallel structure

Parallel and anti-parallel beta-sheets have somewhat different hydrogen bonding patterns.

Hydrogen bonds

Hydrophobic interactions

Ionic bonds

Disulfide bridges (only covalent bond and can be broken by reducing agents)

**denaturing agents can damage all bonds except disulfide

Molecules that stores oxygen in tissues such as muscle

Smaller, single peptide, and single domain

Binds and releases oxygen in a non-cooperative fashion

Contains secondary and tertiary structures, alpha helices only!


Post-translational modification has cyclic phosphorylation and dephosphorylation, serves as a regulatory role, other modifications can serve other roles

Biological catalysts

Most rxns are catalyzed by enzymes which are regenerated during the course of the reaction

Speed up reaction rates

Measurement of the serum levels of numerous enzymes  is used diagnostically. This is because the presence of these enzymes in the serum  indicates that tissue or cellular damage has occurred resulting  in the release of intracellular component into the blood.

catalyzes the dismutationofthe superoxide(O2.-)radicalinto either molecular  oxygen, O2 or to hydrogen  peroxide,H2O2

Cu and Zn

**has a dimeric structure

Major Structural protein, in 1/3 of body proteins

Unusual Triple Helical structure

Has high 35% Gly and 21% Pro plus (hydroxyproline)

Atypical 2nd and quaternary structure

Other structural proteins also rely on structures atypical for globular  proteins

Major component of connective  tissue such as cartilage, tendons, the organic  matrix of bones, and the cornea of the eye

amino acid sequence in collagen is generally  a repeating tripeptide unit, GlyXaa-Pro or Gly-Xaa-Hyp, where Xaa can be any amino acid and adopt a left-handed helical structure with 3 aa per turn

Three of these helices wrap around one another  with a right-handed twist to form

molecules self-assemble into  collagen fibrils and are packed together to form  collagen fibers

** Scurvy, osteogenesis imperfecta, and Ehlers-Danlos syndrome result defects in collagen  synthesis and/or crosslinking*

•  
• ** To mature collage, prolines on collagen are converted to hydroxyproline. This is carried out by the enzyme prolyl hydroxylase.  Prolyl hydroxylase requires vitamin C, ascorbate, for it’s activity.  If you have a deficiency in vitamin C, you will be unable to resynthesize collagen, and get the disease scurvy.