Visualization of Macromolecular Structures (Protein) 1. Introduction: Macromolecules are very large molecules composed of small molecular units. The most common macromolecules are proteins, nucleic acids, carbohydrates and lipids. Proteins are one of the most abundant macromolecule and perform a wide range of biological functions in living system. One main goal of structural biology is to learn more about the chemical and physical properties of macromolecules specially proteins and how they function and interact. Researchers depend on molecular visualizations to study these complex molecules. (Cipriano et al., 2010). In addition, various functions of a protein depend upon the knowledge of its three-dimensional (3D) geometry. Most 3D structures …show more content…
Scientists use this information to explore known molecules as well as predicted molecules to provide new targets and opportunities for future drug development. Moreover, using the information obtained through visualization softwares, one can predict the binding affinities of different molecules as they interact with protein binding sites and can help in the discovery of a new drug (Breda et al., 2007). 2.3. Protein visualization and human diseases: Proteins carry out various biological functions by their interactions between another protein and other molecules. Consequently, they also regulate the signaling pathways and many biochemical processes of living organisms. Mutations involved in these interactions can cause many diseases in human being. Protein visualization will help us know about the molecular mechanisms of these diseases (Gonzalez & Kann., 2012). 3. Protein …show more content…
A model is constructed outside of Protein Explorer with tools such as SWISS-Model and Deep View and then the saved PDB file is loaded into Protein Explorer for visualization. Addition of this feature into Protein Explorer will assist the users to determine the unknown structure of a protein and they do not need to use another software for this attempt. 4.3. Collaborative Cross-Environment Visualization : Protein Explorer does not offer any collaboration features. SnB Visualization software displays the protein structures solved by the Shake-and-Bake algorithm. The software created a collaborative cross platform to distribute multiple datasets across a network and serves as a collaborative viewing and editing tool for 3D protein structures (Ghadersohi, et al., Submission ID: papers_0375). This feature can be adapted into Protein Explorer to allow a real-time visualization of protein structures with multiple clients. This can be helpful for researchers and protein specialists worldwide. 5.
The shape of the protein chains that produce the building blocks and other structures used in life is mostly determined by weak chemical bonds that are easily broken and remade. These chains can shorten, lengthen, and change shape in response to the input or withdrawal of energy. The changes in the chains alter the shape of the protein and can also alter its function or cause it to become either active or inactive. The ATP molecule can bond to one part of a... ... middle of paper ... ...
Pang, A., Warren, M. J. and Pickersgill, R. W. (2011), Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe–4S cluster-binding site. Acta Crystallographica D, 67: 91–96. doi: 10.1107/S0907444910050201
The Structure and Function of Carbohydrates Large biological molecules are called macromolecules, there are giant molecules (polymers) made up of repeating units (monomers). Carbohydrates are one of the main classes of biological molecules. Macromolecule units (monomers) are joined together by condensation reactions and hydrolysis reactions split macromolecules down into their individual units. Carbohydrates are molecules that contain elements of carbon, hydrogen, and oxygen. Carbohydrates have a 2:1 hydrogen to oxygen ratio, there are twice as many hydrogen atoms as oxygen atoms (the same proportion as in water).
Proteogenomics is a kind of science field that includes proteomics and genomics. Proteomic consists of protein sequence information and genomic consists of genome sequence information. It is used to annotate whole genome and protein coding genes. Proteomic data provides genome analysis by showing genome annotation and using of peptides that is gained from expressed proteins and it can be used to correct coding regions.Identities of protein coding regions in terms of function and sequence is more important than nucleotide sequences because protein coding genes have more function in a cell than other nucleotide sequences. Genome annotation process includes all experimental and computational stages.These stages can be identification of a gene ,function and structure of a gene and coding region locations.To carry out these processes, ab initio gene prediction methods can be used to predict exon and splice sites. Annotation of protein coding genes is very time consuming process ,therefore gene prediction methods are used for genome annotations. Some web site programs provides these genome annotations such as NCBI and Ensembl. These tools shows sequenced genomes and gives more accurate gene annotations. However, these tools may not explain the presence of a protein. Main idea of proteogenomic methods is to identify peptides in samples by using these tools and also with the help of mass spectrometry.Mass spectrometry searches translation of genome sequences rather than protein database searching. This method also annotate protein protein interactions.MS/MS data searching against translation of genome can determine and identify peptide sequences.Thus genome data can be understood by using genomic and transcriptomic information with this proteogenomic methods and tools. Many of proteomic information can be achieved by gene prediction algorithms, cDNA sequences and comparative genomics. Large proteomic datasets can be gained by peptide mass spectrophotometry for proteogenomics because it uses proteomic data to annotate genome. If there is genome sequence data for an organism or closely related genomes are present,proteogenomic tools can be used. Gained proteogenomic data provides comparing of these data between many related species and shows homology relationships among many species proteins to make annotations with high accuracy.From these studies, proteogenomic data demonstrates frame shifts regions, gene start sites and exon and intron boundaries , alternative splicing sites and its detection , proteolytic sites that is found in proteins, prediction of genes and post translational modification sites for protein.
Sequence and structural proteomics involve the large scale analysis of protein structure. Comparison among the sequence and structure of the protein enable the identification on the function of newly discovered genes (Proteoconsult, n.d.). It consists of two parallel goals which one of the goals is to determine three-dimensional structures of proteins. Determine the structure of the protein help to modeled many other structures by using computational techniques (Christendat et al., 2000). This approach is useful in phylogenetic distribution of folds and structural features of proteins (Christendat et al., 2000). Nuclear magnetic resonance (NMR) spectroscopy is one of the techniques that provide experimental data for those initiatives. It is best applied to proteins which are smaller than 250 amino acids (Yee et al., 2001). Although it is limited by size constraints and also lengthy data collection and analysis time, it is still recommended as it can deliver strong results. There are two types of NMR which are one-dimensional NMR and two-dimensional NMR. One-dimensional NMR provides enough information for assessing the folding properties of proteins (Rehm, Huber & Holak, 2002). It also helps to identify a mixture of folded and unfolded protein by observing both signal dispersion and prominent peak. Observation in one-dimensional spectrum also obtains information on molecular weight and aggregation of molecule under investigation. In spite of this, two-dimensional NMR are used for screening that reveal structural include binding, properties of proteins. It also provides important information for optimizing conditions for protein constructs that are amenable to structural studies (Rehm et al., 2002). NMR is a powerful tool which it w...
The three-dimensional contour limits the number of substrates that can possibly react to only those substrates that can specifically fit the enzyme surface. Enzymes have an active site, which is the specific indent caused by the amino acid on the surface that fold inwards. The active site only allows a substrate of the exact unique shape to fit; this is where the substance combines to form an enzyme- substrate complex. Forming an enzyme-substrate complex makes it possible for substrate molecules to combine to form a product. In this experiment, the product is maltose.
its original shape and shape. Within the phospholipid bi-layer there are proteins, and these. proteins are made up of polypeptide chains which are joined together. by hydrogen, hydrophobic and peptide bonds. Once the temperature has increased above 40°C the molecules vibrate so energetically that these bonds break easily and therefore create holes within the cell wall.
“This knowledge will help us design drugs that mimic the viral effects on these proteins to either activate a host’s immune response or shut it down,” said Dr. Michael Gale, associate ...
Myoglobin consist of single polypeptide chain that made up of 153 amino acid and ahs a size of 18 kDa. Its three-dimensional structure was first determined by X-ray crystallography by John Kendrew in 1957. Myoglobin is a typical globular protein in that it is a highly folded compact structure with most of the hydrophobic amino acid residues buried in the interior and many of the polar residues on the surface. X-ray crystallography revealed that the single polypeptide chain of myoglobin consist of entirely of eight (labelled A-H) alpha-helical. Within a hydrophobic crevice formed by the folding polypeptide chain is the heme prosthetic group. This nonopolypepetide unit is noncovalently bound to myoglobin and is essential for the biological activity of the protein.
"The Species of the Secondary Protein Structure. Virtual Chembook - Elmhurst College. Retrieved July 25, 2008, from http://www.cd http://www.elmhurst.edu/chm/vchembook/566secprotein.html Silk Road Foundation. n.d. - n.d. - n.d.
Its many contains disulphide bonds, which make it an extremely stable protein. References Website’s used :. www.Intelihealth.com - www. Inteli www.dentistry.leeds.ac.uk/biochem/lectures/nutrition. www.healthy.net/library/books/haas/funct.htm.
A polypeptide chain is a series of amino acids that are joined by the peptide bonds. Each amino acid in a polypeptide chain is called a residue. It also has polarity because its ends are different. The backbone or main chain is the part of the polypeptide chain that is made up of a regularly repeating part and is rich with the potential for hydrogen-bonding. There is also a variable part, which comprises the distinct side chain. Each residue of the chain has a carbonyl group, which is good hydrogen-bond acceptor, and an NH group, which is a good hydrogen-bond donor. The groups interact with the functional groups of the side chains and each other to stabilize structures. Proteins are polypeptide chains that have 500 to 2,000 amino acid residues. Oligopeptides, or peptides, are made up of small numbers of amino acids. Each protein has a precisely defined, unique amino acid sequence, referred to as its primary structure. The amino acid sequences of proteins are determined by the nucleotide sequences of genes because nucleotides in DNA specify a complimentary sequence in RNA, which specifies the amino acid sequence. Amino acid sequences determine the 3D structures of proteins. An alteration in the amino acid sequence can produce disease and abnormal function. All of the different ways
More than 45 million chemical compounds are known and the number may increase in million every year, without cheminformatics, the access of these huge amounts of information is very difficult.
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...
Pre-discovery process is the first stage of drug discovery. During Pre-discovery stage chemists and pharmacologists endeavor to understand and identify the factors which can play a significant role in the particular disease. After revealing the cause of disease or understanding it a target molecule against which drug will act is being chosen. In order to understand the structure the target molecule is eliminated, isolated and its various interactions are inquired. Understanding interactions of the molecule can be helpful in finding treatment of a specific disease. Next stage includes the demonstration that the chosen molecule is relevant to the disease and proof that the drug target is associated with a desired change in the behavior of diseased cells (PPD, 2011).