SOPHIA COLLEGE Protein-DNA Interaction MAYUR GAIKWAD 05/05/2015 INTRODUCTION Protein–DNA interactions play a major role in all fields of genetics from regulation and transcription of individual genes to repair of damaged sequences, even to the stabilization of DNA in chromatin and the replication of entire genomes. It is estimated that 2–3% of prokaryotic and 6–7% of eukaryotic genes code for DNA-binding proteins. Additionally, many of these proteins do not merely bind DNA, but also interact with other proteins and sometimes, as is shown in the example of RNA polymerase, only display theirfull activity when organized in multimeric complexes. SEQUENCE-SPECIFIC DNA BINDING Protein recognition of specific sequences on the DNA double
It contains two binding sites that orient themselves to point towards the centre of the ring. Each subunit contains two domains; an RNA binding domain and an ATP hydrolysis domain. In Rho there is an N terminal domain and a C terminal domain where the N terminal domain contains two subdomains. These are a three helix bundle followed by a five stranded beta barrel. The six C terminal domains have a parallel beta sheet enclosed between multiple alpha helices.
(iii) Charge solvated 2 (CS2): a bi-dentate coordination between the metal cation and neutral L-proline through the nitrogen atom of the imino and the oxygen atom of the carbonyl groups Each structure was fully optimized by density functional theory (DFT) calculations using a nonlocal hybrid B3LYP (Becke-Lee-Parr) exchange correlation functional.34, 35 Then vibrational frequencies were calculated to verify the stationary structure for all the structures. The standard split-valence 6–311++G(d,p) basis set of atomic orbitals was used for all non metal elements; all the metal cations were described using the LANL2DZ relativistic pseudopotentials.36-38 The GAMESS suit of programs was used for all calculations.39 Since group IIB transition metals (Zn2+, Cd2+ and Hg2+) are d10 ions, their complexes have singlet ground states in a closed-shell system. Thermodynamic calculations including enthalpy (∆H), entropy (∆S) and free energy (∆G) terms were also performed at the standard temperature of 298 K and then used for the determination of metal ion affinities (MIA) for each system, which is defined as the negative enthalpy variation (-∆H) of the following coordination process at 298
RESULTS AND DISCUSSION A. Basicity of Amines The lone pair of electrons on nitrogen makes it basic and nucleophilic. (McMurry, 2010) The act as Lewis bases because of the unshared pair of electron. The more unshared pair electron, the more basic the amine is. The trend in the basicity of amines is: primary > secondary > tertiary. Table 1.0 Basicity of Amines Results Amine pH Aniline 7 Benzylamine 11 Diethylamine 9 Table 1.0 shows the result of the basicity of amines according to the experiment conducted.
Amino acids are the building blocks of proteins. All amino acids have the same basic structure but differ in their R-side chains. Each amino acid consists of an amino group (-NH3), a carboxyl group (-COOH) and a hydrogen atom (H). The amino and carboxyl groups are attached to a central alpha carbon together with a hydrogen atom and an R-side chain. There are currently known that over 170 amino acids occur in organisms but only 20 are commonly found in proteins.
Binding of O2 take place with high affinity in an O2 rich environment & O2 leaves Hb in vice versa condition. The co-operative binding process is describe using structure of Hb as follows- Structure of Haemoglobin:- Haemoglobin being an oligomeric compound is composed of four subunits, 2α chain & 2βchain forming alpha helices. Short non helical section connects these helices which are stabilized by hydrogen bonds. Each subunit consists of a heme group in the centre & each heme group is made up of protoporphyrin & iron atom being held in the centre of porphyrin, heterocyclic ring. The ability of Hb to bind O2 is dependent on the presence of this prosthetic heme group, it is where the oxygen binding take place.
In addition, excess amount of carbon should be used to ensure the formation of Mo2C. However, this model is limited only to the formation of Mo2C. In the succeeding sections possible formation of MoC will be discussed as can be seen from the results of this study. Due to this, molybdenum carbide will be denoted as MoxC on this
In compound B, there are two positions of the centre of symmetry. However, the dipole moment canceled each other. In compound C, there are two positions of the centre of symmetry and since fluorine atoms attached are not opposite to each other, their dipole moments do not cancel each other leading to the presence of dipole moments. 7(c) For a compound to have a center of symmetry, the center atom (chiral carbon) must be attached to different four groups which CH4, CH3Cl, CH2ClF lack. CHClFI is chiral since it has four groups attached to chiral carbon (center of symmetry).
Polar amino acids ( acidic, basic, neutral) are hydrophilic & tend to be placed on the out side of the protein. Non-polar ( Hydrophobic) amino acid tend to be placed on the inside of the proteins. It is the fundermental level of protein structure. Its explain the unit amino acid sequence of form carboxyl terminals to amino acid terminal in a protein. Primary structure is very important as it indicates the 3 dimentional structure needed for the biological function of protein.
All forms of DNA store information in DNA words. Basically these words are composed of four characters. These characters are called nucleotides in the biological sciences. Nucleotides are of four types: A (Adenine), C (Cytosine), G (Guanine) and T (Thymine). A four letter combination where each letter can be anyone of the nucleotides represents a DNA word.