advances-in-protein-chemistry

Brownian Dynamics (BD) method
Protein interactions are responsible for most cellular processes. As far as the protein function is concerned, it is necessary to get an
idea that how protein interacts with other molecules in the biological system at the molecular level. Computational and experimental
approaches could be employed for this purpose. Experimental techniques, like nuclear magnetic resonance (NMR) and X-ray
crystallographic analysis are used to explore protein structures that could be accessed through the Protein Data Bank (PDB) on internet.
To determine the structures of macromolecules like protein complexes is more difficult by employing these methodologies. The Brownian
dynamics (BD) method (Monte Carlo approach), has been used to envisage protein interactions. Brownian dynamics was effectively
used to simulate the recognition between scorpion toxins and potassium channels [23]. BD prediction for the interaction between KcsA
potassium channel and scorpion toxin Lq2 has been verified by the potassium channel-charybdo toxin complex structure [24], which
was determined by NMR studies [25].
Various types of methods for protein structural determination and dynamics can be divided into “Experimental Methods” and
“Computational Methods”.
Experimental Methods: Techniques for Analyzing Protein Dynamics
The dynamics and of proteins can be explored at atomic or residue level (amino acids), with the help of established methodologies/
techniques, like hydrogen exchange NMR or Molecular Dynamics simulations. These techniques have supplied the information associating
structure and dynamics but they cannot be applied easily on a proteomic scale and are not able to expose evolutionary linkages clearly.
Free energy estimation-based models are constructive to calculate local properties of protein, such as hydrogen exchange rates [26]. The
technique requires widespread calculations and assessment at residue (amino acids) level of a thermodynamic quantity and the free
energy (ΔG) of folding which is incredibly complex to calculate perfectly even using careful parameterizations. Elastic Network Models
(ENM), are very constructive in exposing slow motions of protein molecules. Such models do not provide specific interactions within the
molecules therefore; can offer limited approaching into the physicochemical properties of highly dynamic protein. Simple and consistent
methods are needed for in silico (computational) analysis that could help to recognize and give details the idea for dynamics of proteins.
Techniques for analyzing protein dynamics:
Fluorescence recovery after photobleaching (FRAP)
Single particle tracking (SPT)
Fluorescence correlation spectroscopy (FCS)
Nuclear Magnetic Resonance (NMR)
X-Ray and Neutron Scattering
Fluorescence Technique
Single Molecule Technique
Hydrogen Exchange Mass Spectrometry
Fourier Transform Infrared (FTIR) Spectroscopy
Circular Dichroism (CD)
Raman Spectroscopy
Dual Polarization Interferometry (DPI)
Crystallographic Analysis
Electron Crystallography
Atomic Force Microscopy
Cryoelectron Microscopy
Above mentioned techniques and established physical models are engaged into data analysis and give extraordinary explanations
of the biophysical characteristics of protein dynamics and micro-domains in cell membranes. In fluorescence imaging methods and
microscope systems are used in green fluorescent protein (GFP) biology that makes it simple to identify the position of GFP fusion
proteins, moreover, to quantify their profusion and to investigate the motion and interactions. Imaging methods like FRAP, FRET and
FCS have been modified that they could be available on commercial scale as user-friendly scanning microscopes. Moreover, computing
resources are available in huge amount and data can be analyzed into digital information with the help of software. The advances in
imaging methods and technical equipment are helpful in providing a marvelous insight for exploring the kinetic properties of proteins
in biological systems.
Nuclear Magnetic Resonance (NMR)
Nuclear magnetic resonance (NMR) spectroscopy is employed to scrutinize the dynamic behavior of a protein at a multitude of
specific sites. Moreover, protein movements on a broad range of timescales can be screened using various types of NMR experiments, like
nuclear spin relaxation rate measurements give insights into the internal motions on fast (sub-nanoseconds) and slow (microseconds, μs
to milliseconds, ms) timescales and generally rotational diffusion of the molecule (5-50 nanoseconds, ns), whereas rates of magnetization
transfer among protons with different chemical shifts and proton exchange give an idea about movements of protein domains on the
very slow timescales (milliseconds to days). X-ray crystallographic analysis and NMR spectroscopic analysis regularly present ideas of
the function of protein.
The high resolution NMR spectroscopy is found to obtain comprehensive information about the structure and dynamics of proteins,
in order to explicate their functions. In order to function accurately, the polypeptide chain must fold into a well-defined, compact
structure (3D structure). In general, non-polar amino acid side chains pack into the hydrophobic interior core of the molecule, while
hydrophilic side chains make up the solvent-accessible protein surface. A folded protein is well planned and well ordered and significant
portions of the protein are often flexible as well. Both well-ordered and flexible protein domains have roles in biological processes. The
3D structure of a protein is specified by the linear sequence of amino acids in the polypeptide chain. Despite progress in predicting the
structure of a protein from its amino acid sequence, experimental methods remain the only reliable means to obtain high-resolution
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