Protein engineering

1. Entropy – enthalpy
compensation;

2. Entropy-enthalpy compensation: Role and ramifications
in biomolecular ligand recognition and design
• The phenomenon of entropy–enthalpy
compensation (referred to hereafter as
compensation) is widely invoked as an
explanatory principle in thermodynamic analyses
of proteins, ligands, and nucleic acids. A far-from-
exhaustive literature search in biological and
chemical databases using the keywords entropy,
enthalpy, and compensation yields >200
references to date. The term entropy-enthalpy
compensation, however, is applied variably in this
literature. The phenomena described by this term
can be grouped into four categories, as follows:

3. • The concomitant increase in S and H with
temperature, basically, a restatement of the
thermodynamic definitions.
• where H, S, and T are the enthalpy, entropy, and
absolute temperatures, respectively, and the
derivatives are taken at constant pressure.
• Depending on whether Cp is temperature
dependent or not and the range of temperatures
examined, a plot of H versus S for a series of
experiments at different temperatures may appear
linear.

4. • “enthalpy–entropy compensation” (EEC) effect has been a long-standing
fascinating yet unresolved phenomenon in chemical thermodynamics.
• the enthalpy (ΔH) and entropy (ΔS) values of “similar processes” are considered
keeping aside the role of the other important thermodynamic parameter, that is,
the free energy (ΔG).
• Considering ΔG along with ΔH and ΔS, it is established that the conventional
EEC plot is not appropriate and mathematically sound.
• Consideration of ΔG may account for correlations of different kinds, linear,
nonlinear, and so forth.
• Reports of non- or anticompensation phenomenon also prevail in the literature.
• A realistic account of the role of ΔG along with ΔH and ΔS in the understanding
of such EEC correlations using authentic literature data is presented and
discussed herein. EEC has several facets.
• Planned studies on similar systems with a wide range of ΔG values are required
for realistic evaluation of the EEC and antienthalpy entropy compensation
manifestations.

5. Entropy-enthalpy compensation as a general phenomenon in thermodynamics.
Three examples of compensating entropic and enthalpic contributions to the free energy
as a function of temperature in general thermodynamic phenomena.
The free energy (G) of the process as a function of temperature is shown, along with
enthalpic (H) and entropic (TS) contributions.
(a) Transfer of neopentane from its neat phase to water (data from figure 3 ref 59),
(b) myoglobin unfolding (data from table 2 of Reference 65), and
(c) protein-protein association (data from figure 3b of Reference 15).
In all three cases, H and TS change substantially
whereas G remains almost constant, suggesting substantial entropy-enthalpy
compensation.

6. • Designing for Improvements in Affinity Directly Is Likely To Be
More Productive
• Through steady progress in computer simulation techniques,
protein-ligand binding free energies can now be computed directly,
without relying on separately estimating enthalpic and entropic
components.
• This avoids difficulties in dealing with the large and often correlated
errors and near cancellations in separate estimates of entropy and
enthalpy.
• Moreover, the computational effort required to compute precise
estimates of free energy differences is often orders of magnitude
less than that required to compute enthalpy differences to the
same precision, even for simple solvated systems.
• To design ligands on the basis of free energy considerations alone,
rather than attempting to design separately for enthalpy or entropy
while factoring in the possibility of entropy-enthalpy compensation.

7. • Small globular protein unfolding Privalov and Gill (1988)
measured the unfolding free energy and enthalpy of
several small proteins using calorimetry, and they found
that H and S of unfolding on a per-residue basis are highly
correlated.
• Calcium binding to proteins Linear S versus H plots obtained
from calcium-binding proteins.
• Unfolding of cytochrome c
• Milne et al. (1999) measured the hydrogen-exchange
protection factors for amide proteins in oxidized and
reduced cytochrome c at various temperatures.
• From the T dependence of these protection factors, they
determined S and H for opening at each amide and found a
high correlation.

8. • Outline of bioengineering of macromolecules a multidisciplinary
approach;
• Computer Simulation for biological and bioengineering purposes is being
referred today also as In silico as a first approach for the In Vitro and In
Vivo expensive and time-consuming tests.
• It is a necessary and fast-growing field of interdisciplinary knowledge to
fulfill today's and future demands, ranging from bioengineering modeling
and simulation of mechanical devices to the more complex and uncertain
field of biofabrication of human tissues and organs towards we call
Medicine 4.0.
• In order to establish models for the phenomena studied, not only the
boundary conditions and mathematical representation of such
• -chemical, biological, biochemical and physical phenomena has to be
implemented, but the computational approach to obtain representative
models and relevant results as a feasible task.
• Such models can bring solutions to one level of complexity according to
the specific problem to be solved.

9. • Molecular engineering is an emerging field of study concerned with
the design and testing of molecular properties, behavior and
interactions in order to assemble better materials, systems, and
processes for specific functions.
• This approach, in which observable properties of a macroscopic
system are influenced by direct alteration of a molecular structure,
falls into the broader category of “bottom-up” design.
material development efforts in
emerging technologies that require
rigorous rational molecular design
approaches towards systems of high
complexity.

10. • A molecular design approach seeks to
manipulate system properties directly using
an understanding of their chemical and
physical origins.
• This often gives rise to fundamentally new
materials and systems, which are required to
address outstanding needs in numerous fields,
from energy to healthcare to electronics.

11. • Molecular design has been an important element of
many disciplines in academia, including
bioengineering, chemical engineering, electrical
engineering, materials science, mechanical engineering
and chemistry.
• However, one of the ongoing challenges is in bringing
together the critical mass of manpower amongst
disciplines to span the realm from design theory to
materials production, and from device design to
product development.
• Thus, while the concept of rational engineering of
technology from the bottom-up is not new, it is still far
from being widely translated into R&D efforts.

12. • Antibiotic surfaces (e.g. incorporation of silver nanoparticles or
antibacterial peptides into coatings to prevent microbial infection)
• Cosmetics (e.g. rheological modification with small molecules and
surfactants in shampoo)
• Cleaning products (e.g. nanosilver in laundry detergent)
• Consumer electronics (e.g. organic light-emitting diode displays (OLED))
• Electrochromic windows (e.g. windows in the Boeing 787 Dreamliner)
• Zero emission vehicles (e.g. advanced fuel cells/batteries)
• Self-cleaning surfaces (e.g. super hydrophobic surface coatings)

13. • On the other hand, it is practically impossible to establish more complex models
for high-level solutions as the ones necessary for complete organisms and organs
simulations,
• for example, due to its complex integration in many levels from molecular to the
high-level behavior of such organisms and organs.
• Therefore, like engineering approach, it is mandatory for future solutions the
integration of multiscale models from molecular to whole organism levels.
• This paper sheds some light on this subject not only proposing a preliminary
framework as a basis for multiscale simulation but also showing, using case
studies, the complexity and necessary simplification for some of those levels
involved in a possible framework from bioengineering to biological multiscale
simulations.
• The case studies presented in this paper are only a small set of models illustrating
the challenges and needs for a complete integrated framework.
• They were developed initially as a specific demand in a stand-alone approach at
3D Technologies Research Group in the Renato Archer Information Technology
Center. DOI: https:/doi.org/10.24243/JMEB/2.5.177

15. • Bioengineering has two different meanings of biochemical and
biomedical engineering.
• The former evolved since a chemical engineer participated in the
mass production of penicillin during the World War II (WWII), while
the latter evolved in the late 1960s from the research related to the
space travel program.
• This volume presents a brief overview of the history of engineering
and chemical engineering and provides a detailed discussion on the
history of bioengineering or biological engineering.
• In addition, current topics in biotechnological research in university
departments of chemical engineering and electrical, mechanical
engineering are discussed, as well as bioengineering or biological
engineering, multidisciplinary approach of musical engineering, and
bioterrorism.

16. The fourth industrial revolution – industry 4.0 [