BY,

PREETHI
PRIYANKA
ARTHY
 Abstract

The study of molecular evolution at the level of

protein-coding genes often entails comparing large
datasets of sequences to infer their evolutionary
relationships.
To underscore the biophysical constraints on natural
selection, we survey effects of protein mutations,
highlighting the physical basis for marginal stability
of natural globular proteins and how requirement for
kinetic stability and avoidance of misfolding and
misinteractions might have affected protein
evolution.
 Introduction
• Biological evolution uses mutations as its basic
working material. Mutations occur in DNA
molecules through various mechanisms. Some
mutations are relatively ‘silent’ whereas others
have a more prominent impact on the biological
function.
• Immediate effect of a mutation is the
alteration of the DNA molecule itself and thus,
possibly, its affinities to bind certain proteins
or RNA.
• Regions of the genome that do encode for a
functional RNA or protein can undergo several
different kinds of mutations.
 REVIEW CONSIDERATION
• Present review focuses primarily on the effect of
point mutations and will consider only proteins and will
consider only proteins but not RNA, although many
general principles of evolution are applicable to both
classes of biomolecules.
• We refer to other authors for the evolution of protein
structures via
• sequence re-arrangements such as domain-wise
evolution.
• the fusion of small peptide fragments or the
‘chimeric’ recombination of fragments that is also
exploited in protein engineering
 REVIEW CONSIDERATION
In this context, a stronger collaboration between the
fields of molecular evolution and protein biophysics in
order to achieve this new and deeper insights into
protein evolution.
The effect of mutations on protein stability or binding
affinities is probably the most promising example of how
biophysics can contribute to a better understanding of
evolution.

A correlation between the ratio and the solvent

exposure of the site in the folded protein structure
has been noted recently.
ω ≡ dN/dS ,
where dN/dS is the ratio of non-synonymous over
synonymous substitution rates.
Enhancing evolutionary methods with
biophysical information
 BIOPHYSICAL
CONSEQUENCES
OF PROTEIN
MUTATIONS
 Mutational effects on the thermodynamic
stability of protein folded states
• Protein with globular folded native
structure
• Thermodynamic stability-folded and
unfolded conformation-determined by
the interaction favoring folded state
and unfolded state.
• The more stable-more difficult to
unfold.
• The conformational diversity is
depicted by funnel like representation
of free energy landscape.

Unfolded protein

Folded proteins
 Effects of mutation on folding kinetics
Folding kinetics can be subject to natural
selection.

folding speeds of α-proteins folding speeds of β-proteins

is increased is decreased

mutants with slower unfolding rates occur

more frequently than mutants with faster
unfolding rates

a positive or negative correlation between

folding rate with occurrence frequency was
not observed

This finding suggests that evolution selects more strongly

for a slower unfolding rate than faster folding rate,
EFFECTS OF MUTATION ON FOLDING
KINETICS

• To implement the mutation

• the structure is computationally
modified
• energy is then re-calculated and
compared against the pre-mutation wild-
type value.
• ΔΔG prediction is widely used to screen
large numbers of mutations

limitation :
ΔΔG prediction consider only a single ‘native’
protein conformation
Interactions and misinteractions

• The biological functions of most proteins

require them to interact with other
proteins and/or other biomolecules .
• Mutations affect these interactions and
can lead to misinteractions.
• More recent examples include mutations
implicated in prion, amyloid and other
misfolding that disrupt or weaken the
proper binding between two proteins
Interactions and misinteractions
A classic example is the glutamic acid to valine mutation
in haemoglobin that causes aggregation of haemoglobin
and consequently sickle-cell anaemia.
 Marginal native stability
• native stability is required for
globular proteins to perform their
biological functions and to avoid
misfolding and aggregation
 Chaperones
• In molecular biology, chaperones are
a class of proteins that assist the
folding and assembly of other
proteins, or even reverse misfolding.
• Many mutant proteins fail to fold or
be expressed in the cell because of
reduced native stability, increased
probability of misinteractions during
folding.
• Mutations that decrease native
stability below a certain threshold
cannot participate in the evolutionary
process even if they possess superior
functionality—provided they are
properly folded
 Applications of biophysics-based
models to understand protein
evolution
• Recent genomic and proteomic
initiatives have greatly advanced our
knowledge of the global sequence–
structure relationship and the
evolution of the primary, secondary,
supersecondary, domain, tertiary and
quaternary/complex structures of
proteins
 Applications of biophysics-based
models to understand protein
evolution
• Protein sequence and structure spaces
• Conformational enumeration
• Model interactions and their biophysical basis
• Predictions and rationalizations
• Energy, entropy, fitness, protein neutral nets and fitness/mortality
landscapes
• Mutational robustness, sequence-space topology and population
evolution
• Evolvability, hidden states and promiscuous functions
• Protein divergence driven by gene duplication and mutational
robustness
• Epistasis and co-evolution of interacting amino acid residues
Evolutionary protein biophysics: evolutionary information benefiting biophysical studies of
proteins

The advances summarized above exemplify

how biophysics can assist in the study of
evolution. In the following, we describe
briefly three examples in which
evolutionary data have assisted in
biophysical studies of proteins. The first
example concerns prediction of mutational
change in protein stability, ΔΔG.
 conclusion
• The aim of this review is to provide a broad sketch
of the fundamental biophysical forces that both
enable and constrain protein evolution.
• Starting with the effects of mutations on protein
stability, folding kinetics, interactions, functional
dynamics, promiscuous functions, conformational
switch and conformational disorder.
• These findings are then linked to broader
evolutionary themes including the global and
local organization of protein sequence and
structure space.