D Structure of a Protein

The 3D structure of proteins is also determined by neutron diffraction. A protein crystal is exposed to the neutron beam, and the position of atoms in a protein is determined by the scattered neutron. Unlike X-ray diffraction, the neutron is scattered by the nucleus of the atom and not by electron therefore, this method yields a different kind of picture at the atomic level than X-ray crystallography. Only a small number of proteins have been analyzed by neutron scattering. One major problem of this method is that only a handful of neutron scattering devices are available in the world. Thus, fewer than a dozen proteins have been analyzed at the atomic level by this method. 

The principle of NMR spectroscopy is based on the magnetic properties of the nuclei of certain atoms. Atoms that contain odd number(s) of protons or neutrons behave like a magnet and possess a spin. Thus, atoms of hydrogen 

NMR was developed independently by Felix Bloch at Stanford University and by Edward Purcell at the Massachusetts Institute of Technology MIT, for which they shared the Nobel Prize in Physics in 1952. NMR has a low resolution with a low signal-to-noise (S/N) ratio, even though the NMR signal provided some information about the nucleus of an atom. This difficulty of NMR was overcome by the application of Fourier transformation by Robert Ernst, and soon, 2D and multidimensional NMR became available Robert Ernst received the Nobel Prize in Chemistry in 1991 for these developments of NMR. Later, Kurt Wuthrich developed NMR suitable for the analysis of the 3D structure of a protein molecule, for which he shared the Nobel Prize in Chemistry in 2002 (Wuthrich 2002). 

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Finally, special mention must be made of Cys, which, when present alone, can be considered to belong to the polar uncharged group described above. It can, however, when correctly positioned within the three-dimensional (3-D) structure of a protein, form disulfide bridges with another Cys residue (Figure 4.2). These are the only covalent bonds, apart from the peptide bond of course, that we usually find in proteins2. 

Distance geometry provides sets of 3-D structures of a protein or nucleic acid that fulfill the constraints. The combination of distance geometry, for generation of molecular starting points, with molecular dynamics computations can yield 3-D models of small proteins with precision equal to X-ray crystallography. This combination of NMR, molecular mechanics, and molecular dynamics can be used to provide a three-dimensional protein structure in a situation where the protein cannot be crystallized or the crystals are not appropriate for X-ray crystallography. 

One of the greatest challenges facing theorists today is the prediction of the 3-D structure of a protein starting from its amino acid sequence. Due to the size and complexity of proteins, theoretical methods currently used to investigate small organic molecules are not directly applicable in the study of protein structure. Current approaches to protein-structure prediction can be broadly classified into a priori and heuristic methods. A number of reviews [1-5] and books [6,7] which address 3-D-structure prediction and theoretical aspects of protein folding are available and should be consulted for additional details. 

A method to define modules in the 3-D structure of a protein molecule based on its distance map (a map giving distances between amino acid residues, alpha carbons) has been established. By application of this method to actin, its 3-D structure is expressed as an assembly of a number of modules. It appears to be composed of a central core and several modules attached to the core surface, as shown in Fig. 12 [53]. The core itself is composed of many modules. However, in this figure, only modules involved in the monomer-monomer interaction to form F-actin are specified. 

One of the best-studied carrier molecules is produced as a primary excretory constituent of the adult male mouse, known from its consistent high concentration as the major urinary protein (MUP). The basic 3-D structure of the protein was initially obtained from a monoclinic crystal of recombinant protein (MUP-I), constructed by induction in a bacterial expression system and purified to homogeneity (Kuser, 1990). A wild type version of MUP finally yielded to NMR analysis a clone of the r-isoform (162 residues) was labelled and compared with the crystal-structure (Lucke et al., 1990). Two views of the molecule... 

The chelate effect in proteins is also important, since the three-dimensional (3-D) structure of the protein can impose particular coordination geometry on the metal ion. This determines the ligands available for coordination, their stereochemistry and the local environment, through local hydrophobicity/hydrophilicity, hydrogen bonding by nearby residues with bound and non-bound residues in the metal ion s coordination sphere, etc. A good example is illustrated by the Zn2+-binding site of Cu/Zn superoxide dismutase, which has an affinity for Zn2+, such that the non-metallated protein can extract Zn2+ from solution into the site and can displace Cu2+ from the Zn2+ site when the di-Cu2+ protein is treated with excess Zn2+. 

Nuclear magnetic resonance (NMR) is a widely utilized technique, which detects the reorientation of nuclear spins in a magnetic field. It can potentially be used to determine the 3-D structure of the protein itself, as well as supplying information on kinetics and dynamics, ligand binding, determination of pK- values of individual amino acid residues, on electronic structure and magnetic properties, to mention only some of the applications. In addition, it can be selectively applied to specific nuclei—1H, 13C, 15N, 19F (often substituted for H as a... 

Protein X-ray crystallography gives a snapshot of the structure of a protein as it exists in a crystal. This technique provides a complete and unambiguous three-dimensional (3-D) representation of a protein molecule. It is important to note that the model generated from a crystallographic study is a static or time-averaged view of the molecular structure. Information about molecular motions can be obtained from precise diffraction data however, the motions of molecules within a crystal are usually severely restricted in comparison to the motions of molecules in solution. 

Prediction of 3-D structure of the protein under investigation After completing the analysis of primary structure, modeling the 3-D structure of the protein is carried out using a wide range of data and CPU-intensive computer analysis. In most cases, it is only possible to obtain a rough model of the protein. This may not be the key to predict the actual structure as several... 

Describe, using a suitable example, each of the following (a) a prosthetic group, (b) a peptide link, (c) a S-S bridge and (d) the tertiary structure of a protein. 

Summary of the various types of interactions that stabilize the tertiary structure of a protein (a) ionic, (b) hydrogen bonding, (c) covalent, (d) London dispersion, and (e) dipole-dipole. 

Nearest-neighbor effects refer to the reciprocal influence of adjacent amino acids on protein folding. In some cases, this term also refers to amino acids that are close in the 3-D structure of the protein (<8-10 A away), but distant in the sequence. Early studies found a nonrandom assorting of amino acids in secondary structures by pair-wise analysis of protein sequences (43). More recently, it was reported that the preference of pairs of amino acids for secondary structure was determined, in part. 

The links provided by the SWISS-PROT entries to other proteomics databases like SWISS-2DPAGE, PROSITE/InterPro and about 30 other databases allow for rapid access to experimental proteomic data, like position and number of protein spots on a 2-D gel, other members of the same family, or the 3-D structure of the protein, etc. 

Protein folding One of the most challenging problems in structural biology is the prediction of the 3-D tertiary structure of a protein from its primary structure. 

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