Friday, May 30, 2014

After Genome, the Proteome: Bangalore Lab Maps Human Protein

Breakthrough could transform understanding of disease — and cure
      Human Genome Sequencing was a major breakthrough for the students, professionals and scientists which revolution the biological sciences along with the emergence of new concept i.e. ‘Genes to Drug’. Scientists did not stop at this point and new project of HUPO  was initiated i.e. mapping the total human proteome. Now with the help of Indian Scientists it has been mapped.
This is the next big thing that genetic researchers have been waiting for after the human genome project. While researchers had felt that mere sequencing of the genes would unlock the mystery of life, the true potential of the human genome mapping could not be realized. Scientists hit a roadblock as not enough was known about the proteins that translate the genetic information into functional units like enzymes and proteins. Most human diseases and aging happen because proteins and enzymes become dysfunctional —nobody fully understands why.
Although India did not participate in the human genome project, completion of a human proteome map by this team now puts India at the forefront of the international efforts to characterize the human proteome and it is a matter for pride for science and scientists working in India.
Indian scientists have identified more than 2,000 proteins that were labeled as ‘missing proteins’ by the international research community as they had never been detected or measured. A remarkable achievement is the identification of almost 200 novel proteins in humans that had not been discovered.

Friday, May 23, 2014



IBRI offers distance courses in Biostatistics and Research Methodology, details are as below...

"An unique course for any Graduate, Researchers, Scientist or Professionals"

About Biostatistics and Research Methodology

The field of biostatistics has become an indispensable tool in improving our understanding of biological process and has a direct impact in ensuring the safety and efficacy of pharmacological and biotechnology products. Bio-statisticians can be found beyond pharmacological or medical research in various fields and industries. In addition, the application of biostatistics is expanding to include several relatively new fields, such as medical imaging, ecological forecasting, and statistical genetics.The emphasis of the specialized certificate is in the application of statistical techniques to the analysis of life sciences data. The course sequences starts with a refresher of basic statistical concepts in Bio-statistics to more advanced topics, including the use of the dominant software for statistical analysis in the field. Students will develop a clear, solid understanding of statistical methods and their applications, along with a good understanding of the available software tools needed to carry out the work. The students will cap their certificate by learning about the purpose of clinical trials and how Bio-statistics is applied to the development, analysis and completion of the clinical trial process including an overview of ICH/FDA statistical regulations, planning and writing the statistical section of the protocol, development and writing of the Statistical Analysis Plan, analyzing clinical trial data and writing the results section of the clinical study report. 
With the aim of filling the gap of knowledge of these fields IBRI has planned to initiate this specialized course with the help of experienced professionals.

Course Objectives

The course aims at:

• Select appropriate study designs to address questions for research.
• Qualitative and quantitative methods; ethnographic studies; case study; PA, RRA, New advances in methods of biomedical and clinical research
• Interpret correctly the results of statistical analyses and critically evaluate the use of statistics in the medical and clinical research.
• Select and apply appropriate statistical techniques for managing common types of medical, biological, clinical and other data types. 

Course Content

  1.Certificate Course in Biostatistics & Research Methodology [6 Months]Rs.7,000/-(including Registration fees)
  2.Comprehensive Course in Biostatistics, Epidemiology & Research Methodology [12 Months]Rs.12,500/-(including Registration fees)
  3.Course Structure:For Above Courses
  4.Exam FeesRs.200/ Per paper

Eligibility: Any Graduate

For Course Modules Click Here

For More details see website

Posted by:Indian Biological Sciences and Research Institute, NOIDA

Thursday, May 22, 2014


Structural Biology                              

         Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and because it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on the molecules' basic composition, or "primary structures." Structural biology is that branch of life science, which deals with the study of molecular structure of biological macromolecules like proteins and nucleic acids.
  Bio molecules are too small to see in detail even with the most advanced light microscopes. The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include:
  • Macromolecular crystallography,
  • NMR,
  • Cryo-electron microscopy (cryo-EM)
  • Multiangle light scattering,
  • Small angle scattering,
  • Ultra fast laser spectroscopy, and
  • Dual Polarisation Interferometry and circular dichroism.
Most often researchers use them to study the static "native states" of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. A third approach that structural biologists take to understanding structure is Bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis. See protein structure prediction.In the past few years it has become possible for highly accurate physical molecular models to complement the in silico study of biological structures.
Structural biology seeks to provide a complete and coherent picture of biological phenomena at the molecular and atomic level. The goals of structural biology include developing a comprehensive understanding of the molecular shapes and forms embraced by biological macromolecules and extending this knowledge to understand how different molecular architectures are used to perform the chemical reactions that are central to life.
In addition, structural biologists are interested in understanding related processes such as protein folding, protein dynamics, molecular modeling, drug design, and computational biology. Central tools used in this research include X-ray diffraction, NMR, electron microscopy, other spectroscopes and biophysical methods, protein expression, bio-physical and bio-organic chemistry, computer science and bioengineering.
 Structural research at MIT includes groups focusing on: modular signaling domains and protein-protein interactions; coiled-coil structure, function, and design; structure of Z-DNA, RNA, and protein-nucleic acid complexes; molecular chaperones that fold and unfold proteins; G-protein mediated signal transduction; and ab initio protein design.
Structural biology seeks to provide a complete and coherent picture of biological phenomena at the molecular and atomic level. The goals of structural biology include developing a comprehensive understanding of the molecular shapes and forms embraced by biological macromolecules and extending this knowledge to understand how different molecular architectures are used to perform the chemical reactions that are central to life.
In addition, structural biologists are interested in understanding related processes such as protein folding, protein dynamics, molecular modeling, drug design, and computational biology. Central tools used in this research include X-ray diffraction, NMR, electron microscopy, other spectroscopes and biophysical methods, protein expression, bio-physical and bio-organic chemistry, computer science and bioengineering.
Protein, one of a large group of nitrogen-rich compounds of high molecular weight that are essential and abundant constituents of living organisms. Proteins make up over 50 per cent of the dry weight of most cells and only plant cells with their high cellulose content are less than half protein. There are many different kinds of proteins, including enzymes, hormones, storage proteins such as those in the eggs of birds and reptiles and in seeds, transport proteins such as haemoglobin, contractile proteins found in muscle, proteins involved in blood clotting and immune defence (antibodies), membrane proteins, and many different types of structural proteins. Despite this overwhelming diversity all proteins are made in the same general manner, as linear chains of amino acids. Each chain of amino acids, which might contain several hundred amino acids in a precise sequence, folds up into a unique three-dimensional shape in which its atoms (mainly carbon, hydrogen, nitrogen, oxygen, and sulphur) adopt precise locations. The astronomical number of possible structures that can be generated in this way produces a huge diversity of properties and functions. From a chemical standpoint, proteins are by far the most structurally complex and functionally sophisticated molecules known.
The word protein is derived from the Greek language and means of primary importance. What are proteins? We are protein. Our hair, our nails, our skin, our blood, our enzymes and hormones are protein; indeed, our bodies contain some ten thousand to fifty thousand kinds of protein. But these proteins are constantly being broken down into amino acids Amino acids, recycled and built a new, even oxidized to some extent to provide energy (1 gram of protein weighs in at 4 calories, the same as carbohydrate). In the typical American diet, about 20 percent of the day's total calories come from protein.
The term “protein” (from the Greek “pre-eminent” or “first”) was first used by the Swedish chemist
Jöns Berzelius in 1838 for the complex organic nitrogen-rich substance found in the cells of all animals and plants. Over the following century these were found to be built from 20 different amino acids and to be linked together in linear polymers, known as polypeptide chains. For many years proteins were thought to be amorphous substances with variable compositions. Progress came with the separation of individual proteins from complex mixtures and the preparation of crystals of pure proteins, such as haemoglobin and the enzyme urease. In the late 1930s, Linus Pauling and Robert Corey in the United States used x-ray diffraction (a technique in which a beam of X-rays is passed through a crystal of the substance and the scattered rays measured) to determine the structures of amino acids and peptides. They also correctly predicted that many amino acid chains would fold into a stable conformation rather like a spiral staircase, now known as an - (alpha-) helix. Another milestone occurred in 1955 when the Cambridge scientist Fred Sanger chemically analysed insulin, a small protein hormone, and showed that it was built from a defined set of amino acids linked together in a unique linear sequence. Everyone now accepts that each kind of protein molecule has its own unique sequence of amino acids.
In 1955 the American Christian Anfinsen reported that the small protein ribonuclease (an enzyme) could spontaneously refold into an active form after being "opened up" by harsh chemicals—evidence that the amino acid sequence of a protein specifies its function. At the same time, on the other side of the Atlantic, scientists were probing the three-dimensional structure of protein molecules. In 1960, John Kendrew and Max Perutz used X-ray diffraction to determine the three-dimensional structures of the oxygen-carrying molecules myoglobin and haemoglobin. These studies led to the concept that linear chains of amino acids fold up to give protein molecules that have always precisely the same structure and function.
The most important function of protein is to build up, keep up and replace the tissues in your body. Your muscles, your organs, and some of your hormones are made up mostly of protein.In the diet, proteins are found primarily in meats, poultry, eggs, milk, rice and beans, although there are some amino acids in vegetables as well.  The body must digest the food and break it down into singular amino acids.  The food protein cannot be absorbed directly, because the food sources have polypeptides with hundreds, or even thousands of amino acids joined together in peptide bonds.  These must be broken down with enzymes into the singular amino acids that the body can absorb, and then combined into the proteins that the body requires.  Heat and processing destroy many amino acids in dietary sources, and not all food sources have all the amino acids necessary for proper metabolic balance.  Vegetarians do not have certain amino acids in their diets, such as Lysine, which is found in eggs and poultry products.  A deficiency in even one amino acid will cause biochemical imbalance creating health problems, and the amino acid(s) should be replaced for good physical and mental health.
Our body is constantly renewing all its cells and components. Some cells, like our blood cells, are all completely replaced every month. Others, are replaced, every couple or few months. The end of a year or so has replaced every Atom in our body replaced, if we are eating a proper diet. Atoms are much like rechargeable batteries. They store Solar Energy, by shifting electrons to higher, more energetic orbits. Our bodies release this stored Solar Energy, by returning electrons to lower more stable orbits. Plants are Nature's primary battery chargers. They collect the sun's energy and store it in the electron orbits of atoms that they have collected from the earth and air. Plants work with possibly more than 28 different atoms to work their magic. At least 40 different atoms have been found in plants, but so far, only 28 have been identified as being needed by humans.
This erector set of atoms is used to form, different; sugars, starches, oils, essential oils, amino-acids, enzymes, Coenzymes, proteins, vitamins, hormones, on and on. Proteins are the primary component of numerous body tissues. They are the main component of muscle tissue. Protein helps muscle development, increases strength and improves athletic performance. Protein also makes antibodies and hemoglobin (responsible for delivering oxygen to your blood cells).
Just to sustain life, we need daily infusions of top-quality proteins because our bodies cannot store them (or their building blocks, the amino acids) the way they store fats. The proteins we eat may be complete, meaning they contain all the amino acids we need and in the portions necessary to good health. Or they may be incomplete (lacking one or more essential amino acids). They are further categorized as simple proteins (containing nothing more than amino acids) or conjugated (amino acids bonded with nonprotein molecules). Collagen, a form of connective tissue, is a good example of a simple protein; hemoglobin, of a conjugated one (it's composed of amino acids plus a heme [Iron] group). It's important to know, too, that proteins can complement one another. That when a food lacking a specific essential amino acid is eaten with another food that supplies the missing amino acid, the result is a high-quality protein. Three examples of these complementary proteins: cooked dried beans eaten with rice, a peanut butter sandwich (i.e., bread plus peanut butter) and split pea soup accompanied by corn bread. When a healthy adult (pregnant women excepted) receives and utilizes the amount of protein he or she needs, that person is said to be in nitrogen equilibrium. Pregnant women and growing children are in positive nitrogen balance, meaning their nitrogen intake exceeds that lost (they need it for growth, building of new tissue). On the other hand, those with illness or injury exhibit negative nitrogen balance because they excrete more nitrogen than they consume. As a general rule, the amount of good-quality protein needed to achieve nitrogen equilibrium is 0.8 grams per day per 2.2 pounds (1 kilogram) of body weight for adults. A dire shortfall of protein leads to marasmus, a severe form of protein-calorie malnutrition common among children in developing countries. What determines the quality, the biological value of protein? The amino-acid mix; specifically, the number, type and proportion. Egg whites, with a biological value of 100, contain the right amount of the right amino acids needed to meet the body's needs. Indeed, they are the standard against which other proteins are measured. Good Sources of Complete Protein: Eggs, meat, fish, poultry, milk and other dairy products.
Proteins are abundant in all organisms and are indeed fundamental to life. The diversity of protein structure underlies the very large range of their function. Proteins make up about 15% of the mass of the average person. Protein molecules are essential to us in an enormous variety of different ways. Much of the fabric of our body is constructed from protein molecules. Muscle, cartilage, ligaments, skin and hair - these are all mainly protein materials.In addition to these large-scale structures that hold us together, smaller protein molecules play a vital role in keeping our body working properly. Haemoglobin, hormones, antibodies, and enzymes are all examples of these less obvious proteins.Whether you are a vegetarian or a ’ meat eater’ you must have protein in your diet. The protein in the food we eat is our main source of the chemical building blocks we need to build our own protein molecules. Proteins are very complicated molecules. With 20 different amino acids that can be arranged in any order to make a polypeptide of up to thousands of amino acids long, their potential for variety is extraordinary. This variety allows proteins to function as exquisitely specific enzymes that compose a cell's metabolism. An E. coli bacterium, one of the most simple biological organisms, has over a 1000 different proteins working at.

The Building Blocks of Protein:

There are nine essential (L-form) amino acids that your body requires and must be obtained from food (or supplementation), since the body cannot manufacture them from other amino acids.  These are Histidine, Isoleucine, Leucine, Lysine, Methionin, Phenylalanine, Threonine, Tryptophan and Valine.

Non Essential Amino Acids

Non-essential amino acids are just as important, but are categorized as non-essential since they can be made within the body from other amino acids.  This biochemical conversion is called transamination.  Generally Pyridoxal 5'Phosphate (active B6) is required for this conversion, and other vitamins and minerals may be also necessary depending on the amino acid.  For example Pyridoxal 5'Phosphate and Vitamin C are necessary to metabolize Lysine into Carnitine.  When the body is lacking sufficient essential amino acids, or there  are insufficient co-factors (vitamins) necessary for transamination, a deficiency of the non-essential amino acid can also exist.  This can create a metabolic imbalance and possible health problems, since there would not be enough of all the amino acids necessary to create the many proteins that the body require for growth and function.  The non essential amino acids are: Alanine, Arginine, Asparagin, Aspartic Acid, Carnitine, Citrulline, Cysteine, Cystine, Gamma-aminobutyric Acid (Gaba), Glutamic Acid, Glutamine, Glycine, Ornithine, Proline, Serine, Taurine, and Tyrosine. Some non-essential amino acids in adults are essential in infants and others become essential when there are conditions in the body that prevent the biochemical conversion of one amino acid into another. It is necessary to constantly replace amino acids to nourish the body and repair and regenerate tissue.  Although we obtain amino acids in food, perfect diets and proper balance are rarely achieved and supplementation is important to keep the body in good health.  Also in times of physical and emotional stress, illness, injury and surgery the body requires more amino acids that can be obtained in foods alone.  In addition, many conditions and lifestyles may cause an imbalance of amino acids and proper balance is critical for good health and longevity.

These are peptide-bonded amino acids from food sources such as whey, casein, milk and eggs.  They may have hundreds or thousands of peptide bonded amino acids, and your body still needs to digest them and break them down into the singular amino acids that the body can utilize.  Some of them never get absorbed.  These predigested proteins will also have the good characteristics from food sources that may cause allergic reactions to food sensitive individuals.UPS Pharmaceutical grade, or the highest quality, pure, crystalline amino acids are the singular L-form amino acids.  The body best utilizes these, since they do not require digestion and are easily absorbed.  The best delivery system is capsules (not tablets), since heat and pressure, which are used in most tablets, can destroy amino acids. A protein molecule is made from a long chain of these amino acids, each linked to its neighbour through a covalent peptide bond. Proteins are therefore also known as polypeptides. Each type of protein has a unique sequence of amino acids, exactly the same from one molecule to the next. Many thousands of different proteins are known, each with its own particular amino acid sequence. The repeating sequence of atoms along the core of the polypeptide chain is referred to as the polypeptide backbone.

Proteins have four levels of configuration. Primary structure, the amino acid sequence, is specified by genetic information. As the polypeptide chain folds, it forms certain localized arrangements of adjacent amino acids that constitute secondary structure. The overall three- dimensional shape that a polypeptide assumes is called the tertiary structure. A protein that consists of more polypeptide chains (or subunits) are said to have a quaternary structure.
Peptide Bonds
Amino acids are linked to each other by peptide bonds. Peptide bonds are formed by the dehydration of the carboxyl group of one amino acid and the amino group of the next. Because of the resonance structure of the electron orbitals on the amino and carboxyl groups, the peptide bond is planar. The dihedral angle between the amino group and the alpha carbon and the alpha carbon and the carboxyl group are free to rotate and these angles are referred to as the phi-psi angles. Glycine, with the smallest side chain, has the most conformational flexibility about the phi-psi angles. Other amino acids are restricted in their rotation due to steric hindrance from the side chains. The rotation of the dihedral angles of side chains about the different bonds, referred to as chi-1, chi-2 etc., are also restricted for different side chain elements. Proline, which in which the side chain is linked back to the backbone is the most restricted; only two conformations are permitted.
Primary Structure:
 The primary structure of a polypeptide is its amino acid sequence. The amino acids are connected by peptide bonds. Primary structure of polypeptide determines the higher levels of structural organization. Amino acids are linked by peptide bonds between α-carboxyl and α-amino groups. When two amino acids residues are linked in the above manner resulting in peptide bonds, is called a dipeptide. Thus many amino acids link together forming a polypeptide in a primary protein structure whose sequence has N terminus and a C terminus. The N terminus is blocked in few cases by acetyl group. This polypeptide sequence from N to the C terminus is the primary protein structure and typically ranges from 100-1500 amino acids long.

Secondary Structure:
Protein secondary structure includes the regular polypeptide folding patterns such as helices, sheets, and turns. The most common types of secondary structure are α- helix and the β- pleated sheets. Both α- helix and the β- pleated sheet patterns are stabilized by hydrogen bonds between the carbonyl and N-H groups in the polypeptide’s backbone.In the 1930s and 1940s, Linus Pauling and Robert Corey determined the X-ray structures of several amino acids and dipeptides in an effort to elucidate the conformational constraints on a polypeptide chain. Both α- helix and the β- pleated sheet called regular secondary structures because they are composed of sequences of residues with repeating f and c values.
The α Helix
Alpha helices are the most well known element of protein structure, proposed by Pauling and confirmed in the first structure determined, myoglobin, and alpha-helices have distinctive patterns of hydrogen bonding and phi-psi angles. They are generally between 5 and 20 residues in length, but some proteins and coiled-coil structures can be considerably longer. The carboxyl groups of the backbone hydrogen bond to the amino group of a residue four amino acids distant along the chain. Alpha helices generally have a pitch of about 3.5 residues per turn, but there are forms of helices with tighter (3 residues per turn) and longer (4 residues per turn). Alpha helices can be coiled about them selves in two coil, three coil and four coil (four helix bundles) conformations. Alpha helices can exist internal in proteins (generally hydrophobic), on the surface of proteins (amphipathic) or in membranes (hydrophobic). Alpha helices can span membranes either singly or in groups.

β Sheets

Beta-strands are an extended form in which the side chains alternate on either side of the extended chain. The backbones of beta-strands hydrogen bond with the backbone of an adjacent beta strand to form a beta-sheet structure. The strands in a beta sheet can be either parallel or anti-parallel and the hydrogen-bonding pattern is different between the two forms. Anti-parallel beta stands are often linked by short loops containing 3-5 residues in highly characteristic conformations. Longer loops are occasionally found where the loop plays an important role in substrate binding or an active site. The antigen-combining site of the immunoglobulin is an important example of this. Beta sheets can be internal to a protein (largely hydrophobic) or on the surface in which case they are amphipathic, with every other amino acid side chain alternating between hydrophobic and hydrophilic nature. The peptide backbone is constrained by steric hindrance, and hydrogen bonding patterns that limit its torsion angles (phi-psi angles) to certain limits. Plots of phi versus psi dihedral angles for amino acid residues are called Ramachandran plots.

They have a rippled or pleated edge-on appearance and for that reason are sometimes called “pleated sheets.” Successive side chains of a polypeptide chain in a β sheet extend to opposite sides of the sheet with a two-residue repeat distance of 7.0 Å. The distance between adjacent amino acids along a β- strand is fully extended. The distance between adjacent amino acids along a β stand is approximately 3.5 Å, In contrast with a distance of 1.5 Å along the α helix. Antiparallel β-pleated sheets are more stable than parallel β-pleated sheets because fully collinear hydrogen bonds form.

  • If extended strands are lined up side by side, H-bonds bridge from strand to strand. Identical or opposed strand alignments make up parallel or antiparallel beta sheets.
  • Antiparallel beta-sheet is significantly more stable due to the well aligned H-bonds.

The Ramachandran Plot

In a polypeptide the main chain N-Calpha and Calpha-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi and psi, respectively. G N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. For each conformation, the structure was examined for close contacts between atoms. Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii. Therefore, phi and psi angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone.

In the diagram above the white areas correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radi. These regions are sterically disallowed for all amino acids except glycine which is unique in that it lacks a side chain. The red regions correspond to conformations where there are no steric clashes, ie these are the allowed regions namely the alpha-helical and beta-sheet conformations. The yellow areas show the allowed regions if slightly shorter van der Waals radi are used in the calculation, ie the atoms are allowed to come a little closer together. This brings out an additional region which corresponds to the left-handed alpha-helix. L-amino acids cannot form extended regions of left-handed helix but occasionally individual residues adopt this conformation. These residues are usually glycine but can also be asparagine or aspartate where the side chain forms a hydrogen bond with the main chain and therefore stabilises this otherwise unfavourable conformation. The 3(10) helix occurs close to the upper right of the alpha-helical region and is on the edge of allowed region indicating lower stability. Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence it frequently occurs in turn regions of proteins where any other residue would be sterically hindered.
Super secondary Structures
Certain groupings of secondary structural elements, called super secondary structures or motifs, occur in many unrelated globular proteins:
·    The most common form of supersecondary structure is the βαβ motif, in which an α helix connects two parallel strands of a β sheet.
·    Another common supersecondary structure, the β hairpin motif, consists of antiparallel strands connected by relatively tight reverse turns.
·    In α-α motif, two successive antiparallel α helices pack against each other with their axes inclined. This permits energetically favorable intermeshing of their contacting side chains. Such associations stabilize the coiled coil conformation of a keratin.
·    Extended β sheets often roll up to form β barrels.

Motifs may have functional as well as structural significance. For example, Michael Rossmann showed that a βαβαβ unit, in which the β strands form a parallel sheet with helical connections, often acts as a nucleotide binding site. In most proteins that bind dinucleotides (such as nicotinamide adenine dinucleotide, NAD11), two such babab units combine to form a motif known as a dinucleotide-binding fold, or Rossmann fold.
Tertiary Structure
The term tertiary structure refers to the unique three- dimensional conformations those globular proteins assumes as a consequence of the interactions between the side chains in their primary structure. The following types of covalent and non-covalent interaction stabilize tertiary structure.
·    Hydrophobic interaction:
·    Electrostatic interactions
·    Hydrogen bonds:
·    VanderWaal force of interaction.
·    Covalent bond.

The most prominent covalent bonds in tertiary structure are the disulfide bridges found in many extracellular proteins. Cysteine has a thiol group (sulfhydryl hroup) i.e., unique among the 20 amino acids in that it often forms a disulfide bond to another cysteine residue through the oxidation of their thiol groups. This Disulfide linkage is an example of covalent interaction.
a) Interpeptide hydrogen bonds. Maintain secondary structure.
b) Disulfide bonds between cysteine residues. According to older definitions these would be included in primary structure as they are covalent bonds. However, primary structure is nowadays considered to be the sequence of the amino acids. In practice disulfide bonds help maintain tertiary or quaternary structures. Since disulfides are easily reduced to -SH groups inside cells, they are of little use in stabilizing intracellular proteins. They are mostly used for extracellular proteins which are exposed to air outside cells.
c) Hydrogen bonds between R-groups, involving e.g. -NH in ring of His, Trp -OH of Ser, Thr, Tyr
-CONH2 of Asn, Gln
d) Ionic bonds (—NH3+ -OOC—) between R-groups of basic and acidic amino acid residues. Relatively few of the possible ionic interactions occur in practice. This is because most polar groups are on the surface of the protein and form hydrogen bonds to the water.

e) Hydrophobic bonds between R-groups. The most important influence on tertiary and quaternary structure. Most proteins fold up so that their polar residues are largely exposed at the surface. The hydrophobic residues are buried inside, away from the water. The internal structure is thus dictated largely by hydrophobic interactions. This is the oil drop model of protein structure. (Note that intrinsic membrane proteins show an inverse conformation). The strength of hydrophobic bonds increases with temperature, hence many subunit proteins tend to come apart at low temperatures. Formation of hydrophobic bonds is driven mostly by entropy. For example, to dissolve a benzene ring in water - ∆G = +4 kcal (∆H = 0, ∆S = -14). Exposed hydrocarbon residues exert an organizing effect on surrounding water molecules. Self association of hydrocarbon residues liberates solvent molecules and so the entropy increases.

Posted by:-Indian Biological Sciences and Research Institute, NOIDA

Wednesday, May 21, 2014

Database and Website Development by Ariff at IBRI


Welcome to the Cancer Phytotherapy Service.We are here to provide you with all the information
you need about phytotherapy for controlling cancer.This is complementary approach perhaps shows
the future of cancer treament especially when metastasis starts.

Phytotherapy is a form of medical treatment which relies on the use of plants, either whole or in the form of prepared extracts and essences. For thousands of years, plants were a primary source of therapeutic medication for cultures all over the world. With the 20th century came the development of synthesization techniques and totally synthetic drugs, causing phytotherapy to fall out of popularity. However, plants still have a very important place in medicine, and they will continue to do so well into the foreseeable future.
This technique involves the study of plants to determine their properties, and the careful application of plants to treat medical problems. Herbal medicine is a form of phytotherapy, and many of the remedies used in homeopathy are also phytotherapeutic in origin. Extracts of plants are also used in the preparation of some commercial pharmaceuticals, as are synthetic drugs which are based on compounds found in plants. Researchers are also constantly studying plants to find new pharmaceutical compounds and potential applications for them.
Quality and safety are also important issues in phytotherapy. Producers want to make products of high quality and reliability so that practitioners will feel comfortable prescribing them, and patients will feel comfortable using them. Due to the lack of regulation over herbal preparations in many nations, reputable producers must also be able to police themselves to confirm that their products are safe for use.
Chemical companies with a vested interest in finding new drugs have scoured the world seeking for new sources of plant material used by indigenous people or as cottage remedies in the treatment of cancer. There have been hundreds of indigenous plants used in traditional therapies in various countries throughout the world over past centuries. Some of them have been tested and are still being trialled in current efforts to find a way of curing cancer, now recognized as a difficult exercise because of the complex nature of the disease.Modern research proves the efficacy of some plants such as astragalus, eleutherococccus, shisandra and shiitake mushroom and many of the plants used traditionally in herbalism.However, there are many more employed by traditional herbalists that can be included in the range of plant material offering value in therapy, sometimes used in herbal extract, sometimes as food, and sometimes as homoeopathic doses.There are particular plants that affect certain types of cancer by improving specific physiological functions. No magic overall formula has been found so far that is applicable to all types of cancer. However, medical and herbal research continues. The University of Wisconsin, for instance lists 150 plants which they have established as having potential value in the treatment of cancer.

Cancer is a genetic disease characterized by uncontrolled cell growth in the absence of cell cycle regulation. Aberrant cell cycle regulation can arise as a consequence of DNA damage. Under normal physiological conditions the uncontrolled growth of damaged cells is restricted by apoptosis. However these cells can escape the regulatory mechanisms of apoptosis as a result of secondary mutations to genes that regulate apoptosis. This DNA damage can be a result of several environmental factors such as stress, smoking, pollution, diet, toxins and endogenous processes such as errors in replication of DNA and chemical instability of certain DNA bases.
 Genetics of Cancer
Only a small number of the approximately 35,000 genes in the human genome have been associated with cancer. Alterations in the same gene often are associated with different forms of cancer. These malfunctioning genes can be broadly classified into three groups. The first group, called proto-oncogenes, produces protein products that normally enhance cell division or inhibit normal cell death. The mutated forms of these genes are calledoncogenes. The second group, called tumor suppressors, makes proteins that normally prevent cell division or cause cell death. The third group contains DNA repair genes, which help prevent mutations that lead to cancer. Proto-oncogenes and tumor suppressor genes work much like the accelerator and brakes of a car, respectively. The normal speed of a car can be maintained by controlled use of both the accelerator and the brake. Similarly, controlled cell growth is maintained by regulation of proto-oncogenes, which accelerate growth, and tumor suppressor genes, which slow cell growth. Mutations that produce oncogenes accelerate growth while those that affect tumor suppressors prevent the normal inhibition of growth. In either case, uncontrolled cell growth occurs.
Oncogenes and Signal Transduction
In normal cells, proto-oncogenes code for the proteins that send a signal to the nucleus to stimulate cell division. These signaling proteins act in a series of steps called signal transduction cascade or pathwayThis cascade includes a membrane receptor for the signal molecule, intermediary proteins that carry the signal through the cytoplasm, and transcription factors in the nucleus that activate the genes for cell division. In each step of the pathway, one factor or protein activates the next; however, some factors can activate more than one protein in the cell. Oncogenes are altered versions of the proto-oncogenes that code for these signaling molecules. The oncogenes activate the signaling cascade continuously, resulting in an increased production of factors that stimulate growth. For instance, MYC is a proto-oncogene that codes for a transcription factor. Mutations in MYC convert it into an oncogene associated with seventy percent of cancers. RAS is another oncogene that normally functions as an “on-off” switch in the signal cascade. Mutations in RAS cause the signaling pathway to remain “on,” leading to uncontrolled cell growth. About thirty percent of tumors including lung, colon, thyroid, and pancreatic carcinomas have a mutation in RAS.
The conversion of a proto-oncogene to an oncogene may occur by mutation of the proto-oncogene, by rearrangement of genes in the chromosome that moves the proto-oncogene to a new location, or by an increase in the number of copies of the normal proto-oncogene. Sometimes a virus inserts its DNA in or near the proto-oncogene, causing it to become an oncogene. The result of any of these events is an altered form of the gene, which contributes to cancer. Think again of the analogy of the accelerator: mutations that convert proto-oncogenes into oncogenes result in an accelerator stuck to the floor, producing uncontrolled cell growth. Most oncogenes are dominant mutations; a single copy of this gene is sufficient for expression of the growth trait. This is also a “gain of function” mutation because the cells with the mutant form of the protein have gained a new function not present in cells with the normal gene. If your car had two accelerators and one were stuck to the floor, the car would still go too fast, even if there were a second, perfectly functional accelerator. Similarly, one copy of an oncogene is sufficient to cause alterations in cell growth. The presence of an oncogene in a germ line cell (egg or sperm) results in an inherited predisposition for tumors in the offspring. However, a single oncogene is not usually sufficient to cause cancer, so inheritance of an oncogene  does not necessarily result in cancer.
Causes of Cancers
The prevailing model for cancer development is that mutations in genes for tumor suppressors and oncogenes lead to cancer. However, some scientists challenge this view as too simple, arguing that it fails to explain the genetic diversity among cells within a single tumor and does not adequately explain many chromosomal aberrations typical of cancer cells. An alternate model suggests that there are “master genes” controlling cell division. A mutation in a master gene leads to abnormal replication of chromosomes, causing whole sections of chromosomes to be missing or duplicated. This leads to a change in gene dosage, so cells produce too little or too much of a specific protein. If the chromosomal aberrations affect the amount of one or more proteins controlling the cell cycle, such as growth factors or tumor suppressors, the result may be cancer. There is also strong evidence that the excessive addition of methyl groups to genes involved in the cell cycle, DNA repair, and apoptosis is characteristic of some cancers. There may be multiple mechanisms leading to the development of cancer. This further complicates the difficult task of determining what causes cancer.

Posted by:Indian Biological Sciences and Research Institute, NOIDA

Saturday, May 17, 2014

Project Training in Bioinformatics/Biotechnology

IBRI a technical unit of EXORDIOR Technical Services Pvt. Ltd. Conducts training programs in interdisciplinary sciences based upon the theme of the story of six blind men touching the elephant at different points and the conclusion could only be derived by combination of sharing of ideas. Therefore today industry is working in interdisciplinary areas and need the trained personnel in interdisciplinary sciences e.g. Bioinformatics is an interdisciplinary subject which direct applications in Biotech, IT, pharma industry etc. with this aim IBRI imparts Project Training in Bioinformatics and objective is
The interdisciplinary nature of our studies is valuable not only for its immediate benefits to our research but also for keeping the door open to diverse career paths in the sciences /arena of life sciences..”
IBRI has established its trustworthiness and acceptability among the students for its quality Bioinformatics Training Programs as our methodology along with framework is beneficial for students to achieve their dream career path.
Importance Bioinformatics Training Program
It is not an exaggeration that in the near future Bioinformatics may well have the potential to limit wet lab experiments and enhance the speed of research for the generation of new information giving a present day direction to the biological science for the betterment of human society.
Applied Bioinformatics has direct implication in developing and implementing research ideas for research in Molecular Biology, Genetics, Biochemistry, Microbiology and other disciplines of Life Sciences. Therefore it becomes imperative for anyone and everyone who wants to make a career in Biotechnology research and Industry to understand and apply Bioinformatics in his research initiative.
Bioinformatics involves integrative or multidisciplinary approach that is inclusive, but not exclusive of computational, mathematical and statistical methods to study, organize, analyze and interpret biological information, at the molecular, genetic and genomic levels. With the diversity required for the subject, it has become imperative to acquire practical knowledge and skills therefore it can said that Bioinformatics Training is important and indispensable not only for Bioinformaticians but also for all the researchers in the Life Sciences arena.
Benefits of the Training
Scientific Research Skills Development for the logical thinking on the research projects and augmenting in-hand biological science process skills enable students to gain practical skilled knowledge is the most important aspect of technology driven science like Bioinformatics. 
Different Programs as per Individual Needs and this is all together a unique innovative approach in trainings, unlike other industrial training programs where you are required to learn as per the working of Industry.
 The training will provide a rich combination of theoretical foundations and practical skills in Bioinformatics build the necessary computational and scientific foundations.

Practical Oriented with stress on the presentations, interactive sessions and Quality Publications is our main motto during internship i.e.  to publish a quality research paper in good impact factor paper by the completion of internship program as it adds weight age to your profile and generates confidence on your thought process.

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 Salient Features
·          Gain insight into the Bioinformatics and Bioservice Industry. 
·         . Get trained by Qualified and Experienced Professionals. 
·         . Get trained in state of the art laboratory.
·         . Gain hands on practical experience. 
·         . Work on projects with real world significance. 
·         .  Get Approved training certificate.
          Persons having a B.Sc. / M.Sc./ B-Tech/ M-Tech/ B.Pharma/ M.Pharma in  Biotechnology, Bioinformatics, Medical Science, Chemistry, Botany, Zoology, Computer science, Pharmacy, Agriculture, Biochemistry, Molecular biology, Medicine and other relevant Qualification in the respective areas are eligible. Doctors, Computer professionals, R&D Scientist having Graduation, Post graduation and PhD qualifications are also encouraged to apply for the Program. Highly motivated undergraduates in their final year may also apply. 

Bioinformatics Training Program
Tailor-Made Cutting-Edge Bioinformatics & its Allied Areas Training Programs For Scientists, Teachers & Students!

          The goal of the Bioinformatics Training Program (BTP) is to prepare students in bioinformatics and applied computational biology by engaging them in cutting-edge collaborative research featuring a strong biological and biomedical application.
    The Aim of the Project Training is to acquaint the Trainees with the software tools and protocols required to work in industry oriented environmental and become competent to handle the projects independently.. The training modules are designed keeping the Industrial requirements into consideration. The program would offer a deep insight into Bioinformatics applied areas and its emerging fields which have direct applications in modern day Pharmaceutical R&D, Biotech, IT industry. IBRI major project areas are mentioned below: 

  • Agro-Informatics
  • Molecular Modeling
  • Phylogenetic Analysis
  • Computational Biology.
  • in-silico Drug Designing.
  • Biodiversity Informatics.
  • Database and Tool Development.
  • Clinical Trials and Data Management.
  • Structural and Functional Genomics.
  • Structural and Functional Proteomics.
  • Waste Water Management(ETP/STP).
Posted by:Indian Biological Sciences and Research Institute, NOIDA