2.8 Protein Structure 4 - Sequence, structure and function

Protein Structure Overview

  • Course Details:

    • Course Code: LSC-10064

    • Date: 17/11/2024

    • Institution: Keele University, School of Life Sciences

Homology in Proteins

  • Definition of Homology:

    • Refers to similarities in sequence and/or structure between two or more proteins or genes.

  • Measurement of Homology:

    • Example: If Protein 1 has 200 amino acids and Protein 2 has 211 amino acids, and 97 are the same, their sequence identity is calculated as 46%.

      • Proteins are homologous based on sequence identity, not simply percentage.

      • Proteins 1 and 2 share a common barrel structure, illustrating structural homology.

Genetic Diseases Linked to Protein Mutations

  • Genetic Mutations:

    • Changes in a single amino acid can lead to diseases. Examples include:

      • Sickle Cell Anemia: Caused by a mutation in hemoglobin (glu6 -> val6), affecting solubility and altering red blood cell shape, leading to blockages in small vessels.

      • Cystic Fibrosis: Caused by a 3 base pair deletion in DNA, removing phenylalanine from a protein, impacting function.

    • Non-lethal genetic defects can be passed on to the next generation.

Evolution of Proteins

  • Understanding Evolution:

    • Protein and nucleic acid sequences aid in studying evolution.

    • Divergent Evolution: Mutual ancestry leads to homologous structures despite mutations.

      • Limits exist on divergence for retaining function.

    • Convergent Evolution: Similar functions/structures arise independently in different lineages.

      • Driven by random mutations which can be beneficial, neutral, or detrimental.

The Role of Pentraxins in Immunity

  • Pentraxins:

    • CRP and SAP are crucial for innate immunity, recognizing debris and components on foreign pathogens.

    • Found in organisms separated by 500 million years of evolution (e.g., horseshoe crab and humans).

    • CRP and SAP show 32% sequence identity with Limulus homologs and 51% identity with human counterparts.

Sequence Homology and Protein Functionality

  • Structural Homology:

    • Proteins with sequence homology often share structural and functional similarities.

    • Example: Cytochrome C, a 104 residue protein involved in respiration, shows invariant residues critical for heme binding.

    • Homology data:

      • Chimpanzee: 100%

      • Rabbit: 91%

      • Cow, Pig, Sheep: 90%

      • Turtle: 86%

      • Moth: 70%

      • Yeast: 57%

Protein Functions Without Structural Homology

  • Diverse Function without Homology:

    • Subtilisin, a bacterial serine proteinase, and chymotrypsin, a mammalian equivalent, serve the same function without sequence/structural similarity except for a catalytic triad (Asp, His, Ser).

Structural Homology without Sequence Identity

  • Examples of Enzyme Structures:

    • Triose phosphate isomerase and 3-dehydroquinase share a classic barrel structure but diverge in sequence and function.

Low Sequence Identity with Similar Functions

  • Folded Conformations:

    • Enzymes like lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH) exhibit similar binding domains (NAD binding), despite low sequence identity.

Protein Sequencing Methods

  • Edman Degradation:

    • Employs phenyl isothiocyanate for identifying 10-20 residues.

    • Although labor-intensive and time-consuming, it's still employed for N-terminal sequencing to identify genes or proteins efficiently.

Cleavage Process in Protein Structure

  • Cleavage Efficiency:

    • Assumptions based on efficient cleavage: 80%.

    • Theoretical outcomes based on uncleaved and cleaved segments of proteins illustrated through reactions and percentages showing the distribution of resultant fragments.

Conclusion

  • Lesson Summary:

    • This session emphasized the complexities of protein structure and function, linking sequence identity to evolutionary, genetic, and functional aspects of proteins.