Applied Crystallography

Structural Biology involves the study of a conglomeration of molecular structure and dynamics of biological macromolecules. Research in Structural Biology aimed at achieving an expansive understanding of key components and processes by using various theoretical and experimental tools such as X-ray Crystallography, NMR spectroscopy etc., This also includes imaging techniques which help in the better determination of structures in a wide range.

Crystallography is used by materials scientists to characterize different materials. In single crystals, the effects of the crystalline arrangement of atoms are often easy to see macroscopically, because the natural shapes of crystals reflect the atomic structure. In addition, physical properties are often controlled by crystalline defects. The understanding of crystal structures is an important prerequisite for understanding crystallographic defects. Mostly, materials do not occur as a single crystal, but in poly-crystalline form (i.e., as an aggregate of small crystals with different orientations). Because of this, the powder diffraction method, which takes diffraction patterns of polycrystalline samples with a large number of crystals, plays an important role in structural determination. Some materials that have been analysed crystallographically, such as proteins, do not occur naturally as crystals. Typically, such molecules are placed in solution and allowed to slowly crystallize through vapor diffusion. A drop of solution containing the molecule, buffer, and precipitants is sealed in a container with a reservoir containing a hygroscopic solution. Water in the drop diffuses to the reservoir, slowly increasing the concentration and allowing a crystal to form. If the concentration were to rise more quickly, the molecule would simply precipitate out of solution, resulting in disorderly granules rather than an orderly and hence usable crystal.

Chemical crystallography is the application of diffraction techniques to the study of structural chemistry. A frequent purpose is the identification of natural products, or of the products of synthetic chemistry experiments; however, detailed molecular geometry, intermolecular interactions and absolute configuration can also be studied. Structures can be studied as a function of temperature, pressure or the application of electromagnetic radiation, or magnetic or electric fields: such studies comprise only a small minority of the total. While the majority of structure analyses are routine, the need to determine structures from increasingly difficult samples continually presents new challenges: limited crystal quality can appear as weak diffraction, disordered atoms, twinning or large regions of diffuse solvent. Some of these difficulties can be at least partially overcome by employing more powerful radiation sources. Because the extent of diffraction depends on the number of electrons an atom has, identifying the positions of hydrogen atoms using X-ray diffraction can be problematic, as can distinguishing atoms with similar atomic numbers.

X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, particularly protein and nucleic acids such as DNA and RNA. In fact, the double-helical structure of DNA was deduced from crystallographic data. The first crystal structure of a macromolecule was solved in 1958, a three-dimensional model of the myoglobin molecule obtained by X-ray analysis. The Protein Data Bank (PDB) is a freely accessible repository for the structures of proteins and other biological macromolecules. Computer programs such as RasMol or Pymol can be used to visualize biological molecular structures. Neutron crystallography is often used to help refine structures obtained by X-ray methods or to solve a specific bond; the methods are often viewed as complementary, as X-rays are sensitive to electron positions and scatter most strongly off heavy atoms, while neutrons are sensitive to nucleus positions and scatter strongly even off many light isotopes, including hydrogen and deuterium. Electron crystallography has been used to determine some protein structures, most notably membrane proteins and viral capsids.

A crystal is a solid material whose constituent atoms, molecules, or ions are arranged in an orderly repeating pattern extending in all three spatial dimensions. Crystal growth is a major stage of a crystallization process, and consists in the addition of new atoms, ions, or polymer strings into the characteristic arrangement of a crystalline Bravais lattice. The growth typically follows an initial stage of either homogeneous or heterogeneous (surface catalyzed) nucleation, unless a "seed" crystal, purposely added to start the growth, was already present. The action of crystal growth yields a crystalline solid whose atoms or molecules are typically close packed, with fixed positions in space relative to each other. The crystalline state of matter is characterized by a distinct structural rigidity and very high resistance to deformation (i.e. changes of shape and/or volume). Most crystalline solids have high values both of Young's modulus and of the shear modulus of elasticity. This contrasts with most liquids or fluids, which have a low shear modulus, and typically exhibit the capacity for macroscopic viscous flow.

The term “Molecular Modelling” serves as an effective tool to visualize and stimulate the three-dimensional structures so as to predict and analyze the behavior and properties of macromolecules from the atomic level to data mining. This technique paves a way to organize compound properties into the database in order to develop novel drug compounds by performing virtual drug screening. Molecular modeling helps in representing molecular structures using computers with the equations of quantum and classical physics which takes to the discovery of new lead components in drugs. 

The three-dimensional structure formed by the Biomolecules is important to study because of the function it does. These structures may range in several scales from individual atoms to entire protein subunit. These macromolecules may decompose into primary, secondary, tertiary and quaternary structures. The scaffolding, fundamental relation between hydrogen bonding may be studied in detail by Structural biologists with the help of techniques namely Cryo-Electron microscopy, X-ray Crystallography etc.,
 

X-ray free-electron lasers (XFELs) open up new potential outcomes for X-beam crystallographic and spectroscopic investigations of radiation-touchy natural examples under near physiological conditions. To encourage these new X-beam sources, customized test strategies and information preparing conventions must be created. The profoundly radiation-touchy photosystem II (PSII) protein complex is a prime focus for XFEL tests intending to concentrate on the instrument of light-actuated water oxidation occurring at a Mn bunch in this complex. We built up an arrancrystalent of instruments for the investigation of PSII at XFELs, including another fluid fly in view of electrofocusing, a vitality dispersive von Hamos X-beam emanation spectrometer for the hard X-beam extend and a high-throughput delicate X-beam spectrometer in light of a reflection zone plate. While our prompt center is on PSII, the techniques we portray here are appropriate to an extensive variety of metalloenzymes. These exploratory advancements were supplemented by another product suite, cctbx.xfel. This product suite considers close constant checking of the exploratory parameters and identifier signals and the itemized examination of the diffraction and spectroscopy information gathered by us at the Linac Coherent Light Source, considering the particular attributes of information measured at a XFEL.

This computational approach aims at providing Sequence-structure function relations using simulations of structure and dynamics and theoretical models in physical sciences. In order to understand the biological interactions, origin, functions, design/controlling mechanisms it is essential to know the structural information. In the identification of Structure and dynamics, Computational structural biology acts as a potential tool.