UNIT 1

STRUCTURAL GENOMICS

It describes the 3-dimensional structure of every protein encoded by a given genome. This
genome-based approach allows for a high-throughput method of structure determination by a
combination of experimental and modeling approaches.

Difference between structural genomics and traditional structural prediction is that structural
genomics attempts to determine the structure of every protein encoded by the genome, rather
than focusing on one particular protein. With full-genome sequences available, structure
prediction can be done more quickly through a combination of experimental and modeling
approaches.

Advantages of structural genomics

Protein function depends on 3-D structure Thus, the high-throughput structure determination
methods of structural genomics have the potential to inform our understanding of protein
[Link] order to determine protein structures. The gene sequence of the target protein can
also be compared to a known sequence and structural information can then be inferred from the
known protein’s structure

DE NOVO METHODS
Completed genome sequences allow every open reading frame (ORF), the part of a gene that is
likely to contain the sequence for the mRNA and protein, to be cloned and
expressed as protein. These proteins are then purified and crystallized, and then
subjected to one of two types of structure determination: X-ray crystallography and
Nuclear Magnetic Resonance (NMR). The whole genome sequence allows for the design of
every primer required in order to amplify all of the ORFs, clone them into bacteria, and then
express them. By using a whole-genome approach to this traditional method of protein structure
determination, all of the proteins encoded by the genome can be expressed at once. This
approach allows for the structural determination of every protein that is encoded by the genome.

Modelling-based methods:
1. ab initio modeling
Uses protein sequence data and the chemical and physical interactions of the encoded amino
acids to predict the 3-D structures of proteins with no homology to solved protein structures. One
highly successful method for ab initio modeling is the Rosetta program, which divides the
protein into short segments and arranges shortpolypeptide chain into a low-energy local
conformation. Rosetta is available for commercial use and for non-commercial use through its
public program, Robetta.
[Link]-based modeling
This modeling technique compares the gene sequence of an unknown protein with
sequences of proteins with known structures. Depending on the degree of similarity
between the sequences, the structure of the known protein can be used as a model for
solving the structure of the unknown protein. Highly accurate modeling is considered to
require at least 50% amino acid sequence identity between the unknown protein and
the solved structure. 30-50% sequence identity gives a model of intermediate-accuracy,
and sequence identity below 30% gives low-accuracy models.

One disadvantage of this method, however, is that structure is more conserved than sequence and
thus sequence-basedmodeling may not be the most accurate way to predict protein structures.

3. Threading
Threading bases structural modeling on fold similarities rather than sequence [Link]
method may help identify distantly-related proteins and can be used to infermolecular functions.
[Link] Structure Databases and Classifications
 Protein Data Bank (PDB): Gives protein sequence and structural information
 UniProt: provides sequence and functional information
 Structural Classification of Proteins (SCOP Classifications): hierarchical-based
Approach
 Class, Architecture, Topology and Homologous superfamily (CATH): hierarchical-based
approach

FUNCTIONAL GENOMICS
Once whole-genome information is available, then identifying the parts to understanding their
function is required ,referred to as 'functional genomics'.
The unique aspect of functional genomics in an organism whose genome in known
completely is the ability to monitor, whether the expression of genes at the RNA or protein level.

TRANSCRIPTOMICS
The study of transcriptomics, also referred to as expression profiling, expression level of mRNAs
in a given cell population, often using high-throughput techniques based on DNA microarray
technology. The use of next-generation sequencing technology to study the transcriptome at the
nucleotide level is known as RNA-Seq. The transcriptome is the set of all RNA molecules,
including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of
cells.
The term can be applied to the total set of transcripts in a given organism, or to the
specific subset of transcripts present in a particular cell type.
Applications
 The transcriptomes of stem cells and cancer cells will help to understand the processes of
cellular differentiation and carcinogenesis.
 Analysis of the transcriptomes of human oocytes and embryos is used to understand
the molecular mechanisms and signaling pathways controlling early embryonic development.

PROTEOMICS
Proteomics is study of proteins, particularly their structures and functions.
The term proteomics was first coined in 1997
The word proteome is ablend of protein and genome, and was coined by Marc Wilkins in 1994
The proteome is the entire complement of proteins, including the modifications made to a
particular set of proteins, produced by an organism or system. This will vary with time and
distinct requirements, or stresses, that a cell or organism undergoes.
The amount of protein produced for a given amount of mRNA depends on the gene it is
transcribed from and on the current physiological state of the cell.
Proteomics confirms the presence of the protein and provides a direct measure of the quantity
present.
Post-translational modifications
Not only translation from mRNA cause differences, but many proteins are also
subjected to a wide variety of chemical modifications after translation. Many of these post-
translational modifications are critical to the protein's function.
Phosphorylation
One such modification is phosphorylation, which happens to many enzymes and structural
proteins in the process of cell signaling causes a protein to become a target for binding or
interacting with a distinct set of other proteins that recognize the
phosphorylated domain. Because protein phosphorylation is one of the most-studied protein
modifications,

Ubiquitination
Ubiquitin is a small protein that can be affixed to certain protein substrates by enzymes called E3
ubiquitin ligases. Determining which proteins are poly-ubiquitinated can be helpful in
understanding how protein pathways are regulated. This is therefore an additional legitimate
"proteomic" study. Similarly, once it is determined which substrates are ubiquitinated by each
ligase, determining the set of ligases expressed in a particular cell type will be helpful.

METABOLOMICIS
Metabolomics is the study of chemical processes involving metabolites.
The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or
organism, which are the end products of cellular
processes. Thus, while mRNA gene expression data and proteomic analyses does not work,
metabolic profiling can give information. One of the challenges of systems biology and
functional genomics is to integrate proteomic, transcriptomic, and metabolomic information to
give a more complete picture of living organisms.
Analytical methods:
 Gas chromatography, especially when interfaced with mass spectrometry (GC-MS), is
one of the most widely used and powerful methods. It offers very high chromatographic
resolution, but requires chemical derivatization for many biomolecules: only volatile
chemicals can be analysed without derivatization. Some large and polar metabolites
cannot be analysed by GC.
  High performance liquid chromatography (HPLC). Compared to GC, HPLC has lower
chromatographic resolution, but it does have the advantage that a much wider range of analytes
can potentially be measured.
 Capillary electrophoresis (CE). CE has a higher theoretical separation efficiency than
HPLC, and is suitable for use with a wider range of metabolite classes than is GC. As for
all electrophoretic techniques, it is most appropriate for charged analytes.
 Mass spectrometry (MS) is used to identify and to quantify metabolites after separation
by GC, HPLC (LC-MS), or CE. GC-MS is the most 'natural' combination of the three,
and was the first to be developed.
Applications:
Toxicity assessment/toxicology
Metabolic profiling (especially of urine or blood plasma samples) can be used to detect the
physiological changes caused by toxic insult of a chemical (or mixture of chemicals).
Functional genomics
Metabolomics can be an excellent tool for determining the phenotype caused by a genetic
manipulation, such as gene deletion or insertion.
Nutrigenomics is a generalised term which links genomics, transcriptomics, proteomics and
metabolomics to human nutrition. In general a metabolome in a given body fluid is influenced by
endogenous factors such as age, sex, body composition and genetics as well as underlying
pathologies.