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PROTEIN STRUCTURE - Coggle Diagram

- - - - Hydrophobic (non polar)
        
        Gycina, alanine, valine, isoleucine, leucine. proline, methionine, phenylalanine, tryptophan
      - Hydrophilic (uncharged polar)
        
        Asparagine, glutamine, serine, threonine, tyrosine, cysteine
      - Acidic (-)
        
        Aspartic, glutamic acid
      - Basic (+)
        
        Lysine, arginine, histidine
    - - Backone torsional angles
        
        phi: N-Ca and Psi: Ca-C allow movement to get conformations. The R groups can limit the rotation of the angles.
        
        omega: peptide bond (covalent) 180º
        
        In proline 0º
    - - X-ray Crystallography
        
        Pros: atomic-level resolution, most common and reliable method, applied to soluble proteins
        
        Cons: requieres crystallization, proteins must be immobilized, cannot study dynamic processes, requires solving the phase problem.
      - Nuclear Magnetic Resonance (RMN)
        
        Pros: proteins in aqueous solutions (preserving natural motility and thermal motion), detects chemical shifts in atomic nuclei giving information of the local electronic environment, ensemble of models
        
        Cons: small-medium proteins, high protein concentrations, complex data analysis, produces an ensemble (no static structure).
      - Cryo-Electron Microscopy (EM)
        
        Pros: large complexes and membrane proteins, near-atomic resolution, less sample preparation.
        
        Cons: historically lower resolution, limited ability to study smaller proteins, expensive equipment.
- - - - This is due to the interactions between aa close to each other.
      - Propensity: how likely is to find the aa relative to the 2 structure
    - - alpha-helix
        
        Also known as 3.6 13 helix, 3.6 aa per turn and 13 atoms involved in each loop
        
        Right-handed helices predominates. Left are typical in sequences rich in glycine.
        
        Local H bonding between the backbone amino group of one residue and the carbonyls of a residue 4 portions away
      - beta strand
        
        Alternating pattern of hydrophobic and polar aa, giving rise to an extended conformation. Two side chains with a 90 degree angle and the torsion between N-Ca-C-N is 120º
        
        Can be arranged to form supersecondary structures
        
        beta sheet
        
        beta strands connected by H bonds. Can be in parallel or anti-parallel orientation.
      - Turns
        
        Sharp change in the direction of the polypeptide chain. It is a crucial role for the 3 structure. Often act as connectors between two regions of 2 structure.
        
        Rich in proline (rigid) and glycine (flexible).
      - 3 10 helix
        
        10 atoms in H bonding (more strained and less optimal geometrically than the alpha helix, so less stable) every 3 aa per turn. It is right-handed. In the N or C terminus of an alpha helix
      - pi helices
        
        especial case of alpha helix, with an extra aa (7)
    - - Drives protein folding by minimizing exposure of hydrophobic side chains to water. The interior of the protein is hydrophobic while the backbone remans polar. At the protein surface, polar side chains and backbone groups form H bonds with water, stabilizing the protein structure.
  - - - Interactions
    - - conserved, self-folding, evolutionary conserved regions within proteins. They are functional units.
      - Motifs: specific patterns or structures that are part of the 3 structure. Small molecules, repeated.
      - Domains: interactions that can be part of 3 or 4 structures. Bigger molecules, autonomous.
  - - - Crucial role in the protein´s function.
- - - - By plotting these angles can be easily see whether angles fall into allowed regions. This helps to confirm if the protein structure is stable or an unusual conformation.
        
        It simplifies the process of validating protein structures.
  - - - Proteins don´t fold randomly. They follow a path along an energy landscape, where certain intermediate states guide the protein in an efficient manner. This reduces the nº of conformations that need to be testes, allowing quick folding.
  - - - To take into account: protein entropy, water entropy, net entropy change (overall entropy change can be positive if the increase in water entry outweighs the decrease in protein entropy).