Protein Structures
Three-Dimensional Structure of Proteins
Protein Structures
Primary Structure:
Amino acid sequence: The linear sequence of amino acids, dictating the protein's unique order and properties.
Connectivity (peptide & disulfide bonds): Covalent bonds linking amino acids (peptide) and cysteine residues (disulfide), crucial for stability
Higher Order Structures:
Secondary Structure: Local spatial arrangement of polypeptide backbone atoms. Secondary Structure: Local spatial arrangement of polypeptide backbone atoms, such as alpha helices and beta sheets.
Tertiary Structure: Three-dimensional structure of an entire polypeptide, including all its secondary structures and loops.
Quaternary Structure: Spatial arrangement of subunits in proteins with multiple polypeptide chains, defining their interactions and organization.
Tertiary Structure: Three-dimensional structure of an entire polypeptide.
Quaternary Structure: Spatial arrangement of subunits in proteins with multiple polypeptide chains.
Five Themes of Protein Structure
Amino acid sequence determines 3D structure: The specific sequence dictates how the protein folds and functions.
Protein's function depends on its structure (structure-function relationship): The three-dimensional shape is critical for its biological activity.
Noncovalent weak interactions stabilize protein structures: Hydrogen bonds, van der Waals forces, and hydrophobic interactions maintain protein shape.
Common structural patterns aid in understanding protein architecture: Recurring motifs like helices and sheets provide insight into protein organization
Secondary structural elements form in response to noncovalent interactions between neighboring amino acids: Local interactions drive the formation of helices, sheets, and turns.
Secondary Structural Elements
Examples: alpha helices, beta pleated sheets, loops and crossovers: Common motifs that contribute to overall protein architecture.
Stability: Stabilized by numerous hydrogen bonds & minimized steric repulsions: Enhances structural integrity and reduces energetic strain.
Amino acid preferences: Specific amino acids favor certain conformations: Certain residues are more likely to be found in specific secondary structures.
Sequence Prediction: Bioinformatics can predict structural propensities based on amino acid sequence.
Proline and glycine are commonly found in protein turns and loops
Glycine favors curvature because it is small
Proline favors curvature because of its strained nature.
Peptide Bond
Planar structure: Rigid due to resonance, ~40% double-bond character: imits conformational flexibility.
Dipole: Partial negative charge on oxygen, partial positive on nitrogen: Contributes to hydrogen bonding.
Rotation: Not freely rotatable but stretchable & bendable: Affects overall protein flexibility.
Single bonds: Bonds adjacent to the peptide bond (Cα-C and N-Cα) can rotate: Allows for conformational variation.
Peptide Confirmation
Dihedral Angles (Torsion Angles):
Phi ($\phi$): Rotation around the N-Cα bond.
Psi ($\psi$): Rotation around the Cα-C bond.
Omega ($\omega$): Rotation around the peptide bond (typically refers to the bend of the bond rather than free rotation).
Nomenclature:
$\psi$ bond: 180° separation is the widest (energetically favorable). 0° is restricted due to steric clashes.
Newman Projection Analog:
Staggered conformation: Lowest energy.
Eclipsed conformation: Highest energy due to steric clashes.
Peptide Groups
Trans conformation: Most peptide bonds adopt this, where successive Cα atoms are on opposite sides of the peptide bond.
Cis conformation: Less stable (8 kJ/mol) due to steric interference.
Proline exception: 6-10% of proline peptide bonds are cis.
Ramachandran Diagram (Rama Plot)
Definition: Indicates allowed conformations through combinations of the dihedral angles psi and phi when proteins fold into their three-dimensional structure for a polypeptide backbone; sterically disallowed regions are also calculated.
Sterically Forbidden Confirmations: Certain combinations of phi and psi bring atoms closer than their Van der Waals distance.
Interpretation:
Colored areas indicate allowable confirmations.
White areas indicate forbidden confirmations.
Secondary Structure Correlation:
Large dihedral angles (+$120$, -$120$): Beta-pleated sheet conformation.
Decreased angles ($-60$, $-60$): Right-handed alpha helix.
$+60$ $60$ combination: Left-handed alpha helix.
0, 0 combination: Absolutely forbidden because of steric clashes.
Exceptions:
Glycine: Smallest amino acid, less hindered, allows for a wider range of dihedral angles.
Proline: Cyclic side chain limits phi values, confirmationally restricted.
There is more allowable region regarding the dihedral angles of polyglycine.
Certain combinations are more common involving proline residues.
Helical Structures
Characterization:
Helical pitch (p): Measured in Angstroms.
Number of repeating units per turn (n).
Helical rise per repeating unit.
Types:
Right-handed.
Left-handed.
Alpha Helix
Definition: A right handed coil with 3.6 residues per turn.
Rise: 5.4 Angstrom pitch, resulting in 1.5 Angstrom rise per residue ($\frac{5.4}{3.6}$). The formula to calculate the rise per residue is:
Characteristics:
R groups protrude outwards to minimize steric repulsion.
Stabilized by numerous hydrogen bonds, and is intrinsically thermodynamically stable.
Every first amino acid NH forms a hydrogen bond with every fourth amino acid CO.
Has a dipole, with the negative end towards the carboxyl terminus and the positive end towards the amino terminus.
Variations:
3\textsubscript{10} helix: Every first CO forms hydrogen bond to every third NH.
Pi ($\pi$) helix: Every first CO forms hydrogen bond to every fifth NH.
Examples:
Ferritin: A blood protein that binds and stores iron, largely alpha-helical.
Keratins: Two alpha helices wind around each other in a left handed sense to create a super helix or coiled coil structure.
Alpha Helix Attributes
Helical pitch: 5.4 angstroms
3. 6 residues per turn
Each residue rises 1.5 angstroms
R groups protrude outwards
Hydrogen bonds are maximized (every first NH bonds to every fourth CO)
Thermodynamically stable
Overall electric dipole
Beta Structures
Beta Sheet:
Hydrogen bonds to another strand to increase stability.
Strands are in maximum extension, with polypeptide backbone alternating up and down.
Side chains alternate between up and down.
Two Common Confirmations:
Antiparallel.
Parallel.
Anti-Parallel Beta Pleated Sheet
Neighboring hydrogen bonded polypeptide chains run in opposite directions.
The hydrogen bonds are almost linear in nature. Hydrogen bonds between the adjacent NHs and COs are satisfied to the fullest capacity.
Parallel Beta Sheet
Strands run in the same direction.
Requires crossovers in order to remain in the same direction.
C=O and N-H bonds are also satisfied, but the hydrogen bonds are angular.
Parallel sheets with fewer than 5 strands are rare.
Comparison
Antiparallel is more thermodynamically stable.
Beta sheets can contain as many as 22 strands.
Strands are not necessarily sequential in the protein sequence.
Each residue rises in 3.5 angstrom
Beta Sheet Examples
Fatty acid binding protein: Collection of anti-parallel beta pleated sheets connecting by a variety of different loops crawl up to form a beta barrel motif.
Triose phosphate isomerase: Parallel confirmation connected through a variety of small helices form a beta barrel cylindrical structure.
Connections Between Alpha Helices and Beta Sheets
Anti-parallel strands are connected through hairpins or loops
Parallel beta strands cross over above or below the plane.
Reverse Turns (Beta Turns)
Non-repetitive loop confirmations on protein.
Located on the protein surfaces.
Involve four amino acid residues or more.
Type I: Position 2 occupied by proline.
Type II: Position 3 occupied by glycine.
Stabilizing hydrogen bonds lock the loop in position.
Glycine and proline are commonly found in loops because glycine is small and proline is strained.
*Note that normally peptide bonds are trans, however, six to ten percent of proline residue do exist in cis.
Omega Loops
Comprise 40-54 amino acid structures
Backbone that loop fills up quickly
Invariably located on protein surface, possibly playing an important role in biological recognition proteins.
Loop helps make an antibody recognize antigen.
Well defined and rigid, never random or disordered.
Amino Acid Propensities
Different amino acids favor different secondary structures
Alanine, glutamate and leucine are present in helices
Valine and isoleucine are present in beta-strands
Glycine, asparagine, proline are found in turns
Branching at the beta carbons destabilize alpha helices because of steric clashes, so valine, threonine, and isoleucine do not favor helices since helices do accommodate steric clashes
Proline disrupt both alpha helices and beta strands because its ring structure restrict to values with limited dehedral, with 60 degrees and only that
Tertiary interactions between far apart residues help specify the secondary structure of a segment
Circular Dichroism (CD) Spectroscopy
Spectroscopic technique to determine the elements of secondary structures in a protein.
It may measure the difference in circular rotation of any form of structural asymmetry which is based on circular polarized light; The light could be separated in two components (electric versus the magnetic waves that travel 90 degrees to each other).
Measures differences in absorption of left-handed vs. right-handed circularly polarized light. The difference in what is known as molar extinction coefficient for left and for right hand has circular polarized life is plotted as a function of wavelength.
Used to determine if proteins are properly folded. It does not give quantitative number of the amount of alpha helix, but rather can tell the percentage out of the 100% is in a helical shape
Alpha helices or beta confirmations has characteristic CD Spectra
Outcome from spectrum: It determines if the protein has 70% of the structure in alpha helical confirmation, 20% in b-stand and the remainder its groups as random coils
Tertiary Structure
Folding of secondary structural elements.
Specifies position of each atoms in protein.
Confirmation, usually deposited by database and usually readily available for internet access.
Must describe the prosthetic arrangement in the three-dimension arrangement with all the atom molecules
Protein Folding
Confirmation of all side chains need to be taken into account.
It is determined from solvent, pH temperature, salt concentrations and environment.
Some proteins fold spontaneously and others need a chaperone.
Interactions That are Responsible for Protein Folding
Noncovalent stabilizing forces contribute to the most stable structure.
Includes
Hydrogen bonding.
Hydrophilic interactions
Electrostatic attraction between oppositely charged groups
Disulfide bond
Only covalent bond that is significant in tertiary structure is the disulfide bond (cysteine residue). The only disulfide from between the bond of the two dimer of two cysteine.
Prosthetic groups that are not an amino group. So a phosphate group, for example, the metal ion. Such as the heme group.
Classification Based On Tertiary Structure
Fibrous Structure
Usually consist of a single type of Secondary Structure for some kind of repeating secondary structure elements over and over again either all alpha helices or all b shoots. No technically repeating itself all over and over again. The black bone of them does not fold back open itself. Therefore extent.
The torso structure is not specified by secondary structural elements or atoms to atom in the side chains because in into either alpha helix or beat this if the side chains puts it outwards.
Most structural properties includes part of the different sells hair, skin, muscle, nails, porcupine needles.
Globular Proteins
Much more complex in shape than in design than the fibrous proteins since fibrous proteins are extended.
These kind of interruptions between the side chain plays an important role when the protein folds together and all these side chains start to interrupt.
The folding frequently brings residues that are separated that are sequence into proximity in that tertiary structure in the native protein Close proximity as we call it, and this globular proteins are
Much larger group of protein than fibrous protein, and these are most common activity functional proteins. They are most enzymes regular proteins, the the storage proteins signal transducers immunoglobulins, they are everything else but the structural.
Fibrous Protein Examples
Import strength and flexibility to a variety of different structures, and the basic structural unit is always always a some kind of simple repetitive. Secondary structural element motif that it keeps repeating itself
Insoluble on water such as hair or skin, for example.
Is a result of a high concentration of hydrophobic residue on both surfaces and the interior of proteins. Includes: Helix Coil, Beta Turn, and Beta Sheet structures.
Collagen and Keratin are the major example of Helix Coils.
Elastin and resilient are the examples for Beta Turning.
Silk are the examples for Beta sheets.
Alpha Keratin
Component of hair, and feathers for various species.
Alpha keratin has right-handed alpha helix, and they intertwine in the center into a left-handed central domain to create coiled coils which are crossed linked by disulfide bonds that for filaments that bundles.
Alpha keratin contains alanin, valine, and leucine.
Permanent wave includes the process of breaking the disulfide bonds into a new one with desired shapes. It is formed and arranged by stylists.
Collagen
Founded tendons and bone matrix to create a triple helix structure with alpha chains.
*Tripeptide sequence is composed of glycine-x-proline or glycine by x/ four hyroxyproline.
*The nutritional value of gelatin is derived from Collagen, but it is not a nutritional product for humans due to a huge variety of amino acids.Four hydroxyproline reside is a very important residue and collagen structure. Virtually one third or is that 1530 and the roline are they are derivatized from prolene in the lysine from the translated by the enzyme either royal hydrociles or Liesel hydrociles, and these two royal and hydroxlice Require ascorbic acid vitamin c as as the coenzyme to maintain their activity.
*We as mammals cannot produce vitamin c since vitamin is important for the consumption of fat and vitamins. Therefore, vitamin D will require every day since it provides 50 to 100 mg per day to maintain healthy scurvy levels.
*Crowding is an only glycine structure that's fit to that central core
*Collagen structure has a poor solubility for water since it is covalently cross-linked. It can not be disulfide as cysteine since collagen is almost devoid of residue.
*Lysyl Oxidate Enzyme
*Converts lysine residue that are to do I the alahhade called lysine
*This a pivot enzyme to cross linking process with in the collagen molecule.
The degree of cross linking particular issue, an issue increases with age, and that is why meat from older animals is tougher and sheer new than the meter of the younger animals.
*Scurvy has a deficiency of Vitamin c, and it has both active hydroxylies with five hydrolysine that's participate
Lysyl oxidase and Vitamin c is important for collagen structure and protei