Download Online Counseling Resource YCMOU ELearning Drive…

Online Counseling Resource
YCMOU ELearning Drive…
School of Architecture, Science and Technology
Yashwantrao Chavan Maharashtra
Open University, Nashik – 422222, India
SEP-SBI074-CP3-04
Introduction
Programmes and Courses
SEP –SBI074-CP3-U03
School of Science and Technology, Online Counseling Resource…
Credits
 Academic Inputs by
Sonali Alkari
Faculty YCMOU Nagpur Centre,
Faculty LAD college P.G. D of Biotechnology
Research officer Ankur Seeds Pvt Ltd
[email protected]
[email protected]
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School of Science and Technology, Online Counseling Resource…
How to Use This Resource

Counselor at each study center should use this presentation to deliver
lecture of 40-60 minutes during Face-To-Face counseling.

Discussion about students difficulties or tutorial with assignments should
follow the lecture for about 40-60 minutes.

Handouts (with 6 slides on each A4 size page) of this presentation should
be provided to each student.

Each student should discuss on the discussion forum all the terms which
could not be understood. This will improve his writing skills and enhance
knowledge level about topics, which shall be immensely useful for end
exam.

Appear several times, for all the Self-Tests, available for this course.

Student can use handouts for last minutes preparation just before end
exam.
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Learning Objectives
 After studying this module, you should
be able to :
 Describe protein folding
 Discuss mechanism of protein folding
 Describe techniques involved in studying
protein folding.
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School of Science and Technology, Online Counseling Resource…
Introduction: Protein Folding
 Each protein begins as a polypeptide, translated from
a sequence of mRNA as a linear chain of amino acids.
 This polypeptide lacks any developed threedimensional structure.
 However each amino acid in the chain can be
thought of having certain 'gross' chemical features.
These may be hydrophobic, hydrophilic, or
electrically charged.
 These interact
with each other and their
surroundings in the cell to produce a well-defined,
three dimensional shape, the folded protein., known
as the native state.
 The
resulting
three-dimensional
structure
is
determined by the sequence of the amino acids.
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School of Science and Technology, Online Counseling Resource…
Folding and Amino Acid Sequence-1
 The mechanism of protein folding is not completely
understood.
 The amino-acid sequence (or primary structure) of a
protein
predisposes
it
towards
its
native
conformation or conformations.
 It will fold spontaneously during or after synthesis.
 While these macromolecules may be regarded as
"folding themselves", the mechanism depends
equally on the characteristics of the cytosol,
including the nature of the primary solvent (water or
lipid), the concentration of salts, the temperature,
and molecular chaperones.
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Folding and Amino Acid Sequence-2
 Most folded proteins have a hydrophobic core in
which side chain packing stabilizes the folded
state, and charged or polar side chains on the
solvent-exposed surface where they interact
with surrounding water molecules.
 It is generally accepted that minimizing the
number of hydrophobic side chains exposed to
water is the principal driving force behind the
folding process.
 Although a recent theory has been proposed
which reassesses the contributions made by
hydrogen bonding.
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Folding and Amino Acid Sequence-3
 The process of folding in vivo often begins cotranslationally, so that the N-terminus of the
protein begins to fold while the C-terminal
portion of the protein is still being synthesized
by the ribosome.
 Specialized proteins called chaperones assist in
the folding of other proteins.
 A well studied example is the bacterial GroEL
system, which assists in the folding of globular
proteins.
 In eukaryotic organisms chaperones are known
as heat shock proteins.
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School of Science and Technology, Online Counseling Resource…
Mechanism of Protein Folding:1
 Scientists have been able to study many identical
molecules folding together en masse.
 At the coarsest level, it appears that in transitioning
to the native state, a given amino acid sequence takes
on roughly the same route and proceeds through
roughly the same intermediates and transition states.
 Often folding involves first the establishment of
regular secondary and supersecondary structures,
particularly alpha helices and beta sheets, and
afterwards tertiary structure.
 Formation of quaternary structure usually involves the
"assembly" or "coassembly" of subunits that have
already folded.
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Mechanism of Protein Folding:2
 The regular alpha helix and beta sheet
structures fold rapidly because they are
stabilized by intramolecular hydrogen bonds,
as was first characterized by Linus Pauling.
 Protein folding may involve covalent bonding
in the form of disulfide bridges formed
between two cysteine residues or the
formation of metal clusters.
 Shortly before settling into their more
energetically favourable native conformation,
molecules may pass through an intermediate
"molten globule" state.
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School of Science and Technology, Online Counseling Resource…
Protein Folding
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School of Science and Technology, Online Counseling Resource…
Facts of Protein Folding-1
 The essential fact of folding, however, is that
the amino acid sequence of each protein
contains the information that specifies both the
native structure and the pathway.
 This is not to say that identical amino acid
sequences always fold similarly.
 Conformations differ based on environmental
factors as well; similar proteins fold differently
based on where they are found.
 Folding is a spontaneous process independent
of energy inputs from nucleoside triphosphates.
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School of Science and Technology, Online Counseling Resource…
Facts of Protein Folding-2
 The passage of the folded state is mainly
guided by hydrophobic interactions, formation
of intramolecular hydrogen bonds, and van der
Waals
forces,
and
it
is
opposed
by
conformational
entropy,
which
must
be
overcome
by
extrinsic
factors
such
as
chaperones.
 Some proteins never fold in cells at all except
with the assistance of chaperone molecules,
which either isolate individual proteins so that
their folding is not interrupted by interactions
with other proteins or help to unfold misfolded
proteins, giving them a second chance to refold
properly.
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School of Science and Technology, Online Counseling Resource…
Disruption of the Native State-1
 In certain solutions and under some conditions
proteins will not fold into their biochemically
functional forms.
 Temperatures above (and sometimes those below)
the range that cells tend to live in will cause
proteins to unfold or "denature" (this is why boiling
makes the white of an egg opaque).
 High concentrations of solutes, extremes of pH,
mechanical forces, and the presence of chemical
denaturants can do the same.
 A fully denatured protein lacks both tertiary and
secondary structure, and exists as a so-called
random coil.
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Disruption of the Native State-2
 Under certain conditions some proteins can
refold; however, in many cases denaturation is
irreversible.
 Cells sometimes protect their proteins against
the denaturing influence of heat with enzymes
known as chaperones or heat shock proteins,
which assist other proteins both in folding and
in remaining folded.
 This function is crucial to prevent the risk of
precipitation
into
insoluble
amorphous
aggregates.
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School of Science and Technology, Online Counseling Resource…
Techniques for Studying Protein Folding
 Modern studies of folding with high time
resolution.
 Energy landscape theory of protein
folding.
 Computational
prediction
of
protein
tertiary structure.
 Techniques for determination of protein
structure
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Modern Studies of Folding with High Time Resolution
 The study of protein folding has been greatly
advanced in recent years by the development
of fast, time-resolved techniques.
 These are experimental methods for rapidly
triggering the folding of a sample of unfolded
protein, and then observing the resulting
dynamics.
 Fast techniques in widespread use include
ultrafast mixing of solutions, photochemical
methods,
and
laser
temperature
jump
spectroscopy.
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School of Science and Technology, Online Counseling Resource…
Energy Landscape Theory of Protein Folding-1
 The protein folding phenomenon was largely an
experimental endeavor until the formulation of
energy landscape theory by Joseph Bryngelson
and Peter Wolynes in the late 1980s and early
1990s.
 This approach introduced the principle of
minimal frustration, which asserts that evolution
has selected the amino acid sequences of natural
proteins so that interactions between side chains
largely favor the molecule's acquisition of the
folded state.
 Interactions that do not favor folding are
selected
against,
although
some
residual
frustration is expected to exist.
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School of Science and Technology, Online Counseling Resource…
Energy Landscape Theory of Protein Folding-2
 A consequence of these evolutionarily selected
sequences is that proteins are generally thought
to have globally "funneled energy landscapes"
(coined by José Onuchic) that are largely
directed towards the native state.
 This "folding funnel" landscape allows the
protein to fold to the native state through any of
a large number of pathways and intermediates,
rather than being restricted to a single
mechanism.
 The theory is supported by both computational
simulations of model proteins and numerous
experimental studies, and it has been used to
improve methods for protein structure prediction
and design.
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School of Science and Technology, Online Counseling Resource…
Computational Prediction of Protein Tertiary Structure1
 De
novo
or
ab
initio
techniques
for
computational protein structure prediction is
related to, but strictly distinct from, studies
involving protein folding.
 Molecular Dynamics (MD) is an important tool
for studying protein folding and dynamics in
silico.
 Because of computational cost, ab initio MD
folding simulations with explicit water are
limited to peptides and very small proteins.
 MD simulations of larger proteins remain
restricted to dynamics of the experimental
structure or its high-temperature unfolding.
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Computational Prediction of Protein Tertiary Structure-2
 In order to simulate long time folding
processes (beyond about 1 microsecond), like
folding of small-size proteins (about 50
residues) or larger, some approximations or
simplifications in protein models need to be
introduced.
 An
approach
using
reduced
protein
representation
(pseudo-atoms
representing
groups of atoms are defined) and statistical
potential is not only useful in protein structure
prediction, but is also capable of reproducing
the folding pathways.
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School of Science and Technology, Online Counseling Resource…
Techniques for determination of Protein Structure
 The determination of the folded structure of a
protein is a lengthy and complicated process,
involving methods like X-ray crystallography
and NMR.
 One of the major areas of interest is the
prediction of native structure from amino-acid
sequences alone using bioinformatics and
computational simulation methods.
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School of Science and Technology, Online Counseling Resource…
Incorrect Protein Folding & Neurodegenerative Disease
 Misfolded proteins are responsible for prionrelated illnesses such as Creutzfeldt-Jakob
disease, bovine spongiform encephalopathy
(mad cow disease), amyloid-related illnesses
such as Alzheimer's Disease, and a number of
other forms of proteopathy such as cystic
fibrosis.
 These diseases are associated with the
multimerization of misfolded proteins into
insoluble, extracellular aggregates and/or
intracellular inclusions; it is not clear whether
the plaques are the cause or merely a symptom
of illness.
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School of Science and Technology, Online Counseling Resource…
What You Learn…
 You have learnt :
 The Interaction of hydrophobic, hydrophilic, or
electrical charges of protein sequences with each
other and their surroundings in the cell to produce
a well-defined, three dimensional shape, the
folded protein.
 The mechanism of protein folding is not
completely understood.
 Specialized proteins called chaperones assist in
the folding of other proteins.
 Folding is a spontaneous process independent of
energy inputs from nucleoside triphosphates.
 "folding funnel" landscape allows the protein to
fold to the native state through any of a large
number of pathways and intermediates, rather
than being restricted to a single mechanism.
© 2008, YCMOU. All Rights Reserved.
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School of Science and Technology, Online Counseling Resource…
Critical Thinking Questions
1. Describe in details what is protein
folding.
2. Describe the
folding
mechanism
of
protein
3. State the facts of protein folding.
4. Describe the various
techniques
involved in protein folding .
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School of Science and Technology, Online Counseling Resource…
Hints For Critical Thinking Question
1. The Interaction of hydrophobic, hydrophilic,
electrical charges of protein sequences
or
2. Folding involves first the establishment of regular
secondary and supersecondary structures, particularly
alpha helices and beta sheets, and afterwards tertiary
structure.
3. Folding
is a spontaneous process independent of
energy inputs from nucleoside triphosphates.
4. High time resolution, Energy landscape theory,
Computational
prediction
and
Techniques
for
determination of protein structure.
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School of Science and Technology, Online Counseling Resource…
Study Tips:1
 Book1
 Title: Molecular Cell Biology
 Author: Harvey Lodish, David Baltimore
Publisher:Publishers: W. H. Freeman and
Company
 Book2
 Title: Principles of Biochemistry
 Author: AlbertL Lehninger
 Publisher:CBS Publishers & Distributors
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School of Science and Technology, Online Counseling Resource…
Study Tips:2
 Book3
 Title: Biochemistry
 Author: Lubert stryer
 Publishers: Freeman International
 Book4
 Title: Biochemistry
 Author: Keshav Trehan
 Publishers: Wiley Eastern
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School of Science and Technology, Online Counseling Resource…
Study Tips
www.en.wikipedia.org
Microsoft Encarta Encyclopedia
http://en.wikipedia.org/wiki/
Wikipedia the free encyclopedia
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School of Science and Technology, Online Counseling Resource…
End of the Presentation
Thank You
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