Question

11. What are some key properties of a crystal. How does this allow us to gather 3D information about proteins? (500 words)

Answer 1

Protein crystallization is the process of formation of a regular array of individual protein molecules stabilized by crystal contacts. Once formed, these crystals can be used in structural biology to study the molecular structure of the protein, particularly for various industrial or medical purposes. 3D structure of a protein is determined by its amino acid sequence. The most important forces stabilizing the specific 3D structure maintained by a given protein are non-covalent interactions. Crystals differ in physical key properties i.e in hardness, cleavage, optical properties, heat conductivity, and electrical conductivity.

3D structures of proteins are precious source of information which is based on crystal properties involves shape and domain structure, protein classification, prediction of function for uncharacterized proteins, interaction with macromolecules and with small ligands, evidence for enzyme mechanism, structure based drug development, experimental evidence for transmembrane domains.

Basics of protein- structure includes primary, secondary, tertiary, quaternary with different characteristics. The folding pattern of a polypeptide chain can be described in terms of the angles of rotation around the main chain bonds. Key facts about this is chemical bonds have characteristics lengths, the peptide bond haa partial double-bond character. For structural similarity arises due to divergent evolution and convergent evolution.

Proteins with similar sequences have similar 3D- structures. Proteins with similar 3D structure are likely to have similar function. Proteins with similar function can have entirely different sequences. Based on crystals properties 3D structure of proteins determined by X-ray crystallography which has advantage of hugh resolution, no protein mass limit. NMR which have advantages of dynamic aspects, conformation of protein in solution. Electron microscopy have advantages of direct image. Crystallization of proteins can also be useful in the formulation of proteins for pharmaceutical purposes.

Electron crystallography could provide a powerful means for structure determination with such crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields coulomb potential maps rather than electron density maps, it could provide a unique method to visualise the charged states of amino acid residues and metals. A methodology develop for electron crystallography of 3D protein crystals and present the coulomb potential maps at various resolution, respectively, obtained from calcium ATPase and catalase crystals.

Many powerful techniques are used to study the structure and function of a protein . To determine the 3D structure of a protein in atomic resolution, the large proteins have to be crystallised and studied by X-ray diffraction. The structure of small proteins in solution can be determined by NMR analysis because proteins with similar structure often have similar functions, the biochemical activity of a protein can sometimes be predicted by searching for known proteins that are similar in their amino acid sequences.

Further clues to the function of a protein can be derived from examining it's subcellular distribution. Fusion of the protein with a molecular tag, such as the GFP , allows one to track its movement inside the cell. Proteins that enter the nucleus and bind to DNA can be further characterized by footprint analysis, a technique used to regulatory sequences the protein binds to as it controls gene transcription.

All proteins function by binding to other proteins or molecules, and many methods exist for studying protein-protein interactions and identifying potential protein partners. The identity of the proteins recovered from any of these approaches is then ascertained by determining the sequence of the protein or its corresponding gene.