Pulsed EPR Analysis of the Photo-Induced Triplet Radical Pair in the BLUF Protein SyPixD: Determination of the Protein–Protein Distance and Orientation in the Oligomeric Protein

A photo-induced radical pair of FADH^· and Y8^· and in BLUF protein SyPixD was studied by pulsed electron paramagnetic resonance (EPR) spectroscopy. Blue light illumination at 150 K for 30 min followed by cooling to 50 K during illumination induced the stable radical pair. The EPR signal has been characterized by a Pake doublet signal with complete S = 1 spin state. The radical pair was utilized as a probe to analyze the oligomer of SyPixD. The relative arrangement of PixD proteins in the complex was investigated by pulsed electron–electron double resonance (PELDOR) with the orientation selection. Based on the decameric structure in the crystal, the possible structure for the PELDOR results was discussed.     

Protein Folding in Nano-Sized Cylinders

The folding of a model protein confined in a nano-sized cylinder is studied by the off-lattice Go^-like model. The entropy and anisotropy effects of confinement on thermodynamics and dynamics for folding are investigated. Our results show that due to reduction of the search on conformations, the folding rate can be sped up and the thermodynamic stability is enhanced at the cost of the decrease of folding cooperativity. In addition, it is found that these are shape-dependent. Folding is optimized in a cylinder with an appropriate shape when the volume is fixed. This is probably related to the shape of the protein molecule. Furthermore, our results also suggest that there is an orientational transition for the protein molecule following the variation of the radius of cylinder.     

How Is a Protein Molecule Nearsighted？

The effect range of a local change of a protein molecule is calculated using a cluster method developed in this work based on the Gaussian software. This range is found to be about 8A°, which gives a concrete estimation on the “nearsightedness” by Kohn for protein molecules. The cluster method can be applied to calculation of the electronic density of a large molecule such as a motor protein and can provide a basis for the dynamical analysis of a single protein molecule.     

Scaling Behaviour of Conserved Sites in Protein Families

Base on the database of families of structurally similar proteins, a statistical study is made on the scaling behaviour of occupying probabilities of conserved sites (Pc) in various protein families. A power-law decrease of Pc with the increasing protein-chain length Lf is found. This is related to the power-law scaling behaviour of the occurring probabilities of local contact interactions (Plocal) between residues. In addition, applying residue grouping, we find the same scaling behaviour when the number of residue types is more than 12, indicating that 12 residue types are enough to present the complexity of proteins.     

Protein–protein docking with interface residue restraints

The prediction of protein–protein complex structures is crucial for fundamental understanding of celluar processes and drug design. Despite significant progresses in the field, the accuracy of ab initio docking without using any experimental restraints remains relatively low. With the rapid advancement of structural biology, more and more information about binding can be derived from experimental data such as NMR experiments or chemical cross-linking. In addition, information about the residue contacts between proteins may also be derived from their sequences by using evolutionary analysis or deep learning. Here, we propose an efficient approach to incorporate interface residue restraints into protein–protein docking, which is named as HDOCKsite. Extensive evaluations on the protein–protein docking benchmark 4.0 showed that HDOCKsite significantly improved the docking performance and obtained a much higher success rate in binding mode predictions than original ab initio docking.     

Designability of Protein Structures on the Hexagonal Lattice Model

In view of the bonding angle and the number of neighbouring sites, the hexagonal lattice model is preferred to investigate the designability of protein structures. Here we simulate the designable structures by the simplified HP model in a two-dimensional hexagonal lattice with an unrestricted boundary. The result shows that the structures with a large number of core sites correspond to the high designability and have circular-like profiles. The maximum and average designabilities for the hexagonal lattice model are much higher than those for thesquare lattice mode, and the maximum and average designabilities for the square lattice model are much higher than those for the triangle lattice model.     

Protein aggregation and misfolding: good or evil?

Protein aggregation and misfolding have important implications in an increasing number of fields ranging from medicine to biology to nanotechnology and material science. The interest in understanding this field has accordingly increased steadily over the last two decades. During this time the number of publications that have been dedicated to protein aggregation has increased exponentially, tackling the problem from several different and sometime contradictory perspectives. This review is meant to summarize some of the highlights that come from these studies and introduce this topical issue on the subject. The factors that make a protein aggregate and the cellular strategies that defend from aggregation are discussed together with the perspectives that the accumulated knowledge may open.     

Protein–membrane interactions investigated with surface-induced fluorescence attenuation

Research on protein–membrane interactions has been undeveloped due to the lack of proper techniques to detect the position of proteins at membranes because membranes are usually only about 4-nm thick. We have recently developed a new method named surface-induced fluorescence attenuation(SIFA) to track both vertical and lateral kinetics of a single labelling dye in supported lipid bilayers. It takes advantage of strong interaction between a light-emitting dye and a partially reflecting surface. By applying the technique to membrane proteins being fluorescently labelled at different residues, here we show that SIFA can measure not only the insertion depth of a dye inside a lipid bilayer, but also the position of a dye in solution near the surface. SIFA can therefore be used to study membrane proteins of various types.     

Measurement of Binding Force between Microtubule-Associated Protein and Microtubule

Microtubule-associated proteins （MAPs） are important proteins in cells. They can regulate the organization, dynamics and function of microtubules. We measure the binding force between microtubule and a new plant MAP, i.e. AtMAP65-1, by dual-optical tweezers. The force is obtained to be 14.6 ± 3.5 pN from the data statistics and analysis. This force measurement is helpful to understand the function and mechanism of MAPs from the mechanical point of view and lays the groundwork for future measurements of the mechanical properties of other biological macro-molecules.     

Dynamical Analysis of Protein Regulatory Network in Budding Yeast Nucleus

Recent progresses in the protein regulatory network of budding yeast Saccharomyces cerevisiae have provided a global picture of its protein network for further dynamical research. We simplify and modularize the protein regulatory networks in yeast nucleus, and study the dynamical properties of the core 37-node network by a Boolean network model, especially the evolution steps and final fixed points. Our simulation results show that the number of fixed points N（k） for a given size of the attraction basin k obeys a power-law distribution N（k） χ k^-2.024. The yeast network is more similar to a scale-free network than a random network in the above dynamical properties.     

Nonlinear Correlations of Protein Sequences and Symmetries of Their Structures

We investigate the nonlinear correlations of protein sequences by using the nonlinear prediction method developed in nonlinear dynamical theory. It is found that a lot of protein sequences show strong nonlinear correlations and have deterministic structures. Further investigations show that the strong nonlinear correlations of these protein sequences are due to the symmetries of their tertiary structures. Furthermore, the correlation lengths of the sequences are related to the degrees of the symmetries. These results support the duplication mechanism of protein evolution and also reveal one aspect how amino acid sequences encode their spatial structures.     

Nonlinear Dynamics Approach to the Correlation Analysis of Protein Sequences

To clarify the randomness of protein sequences,we make a detailed analysis of a set of typical protein sequences representing each fold by using the nonlinear prediction method developed in nonlinear dynamics theory.No deterministic structures are found in these protein sequences and this implies that they behave as random chains.We also explain the controversial results obtained in previous investigations.     

Protein imprinted polymer using acryloyl-β-cyclodextrin and acrylamide as monomers

A novel protein imprinted polymer was prepared using acryloyl-β-cyclodextrin (β-CD) and acrylamide as monomers on the surface of silica gel. The bovine hemoglobin was used as template and β-CD was allowed to self-assemble with the template protein through hydrogen bonding and hydrophobic interaction. Polymerization was carried out in the presence of acrylamide as an assistant monomer, which resulted in a novel protein imprinted polymer. After removing the template, imprinted cavities with the shape and spatial distribution of functional groups were formed. Bovine serum albumin (BSA) cytochrome c (Cyt) and lysozyme (Lyz) were employed as non-template proteins to test the imprinting effect and the specific binding of bovine hemoglobin to the polymer. The results of the adsorption experiments indicated that such protein imprinted polymer, which was synthesized with β-CD and acrylamide as monomers, could selectively recognize the template protein.     

Bio-energy in s-Helix Protein Molecules with Three Properties of Soliton-Transported Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the a-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of a-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the a-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

Properties of Soliton-Transported Bio-energy in α-Helix Protein Molecules with Three Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of α-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the α-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

Applications of Oblique-Incidence Reflectivity Difference Method in Primary Study of Protein Biomolecules

Oblique-incidence reflectivity difference （OI-RD） analysis is applied to detect the immunoglobulin-G and cytochrome biomolecules on standard glass substrates without fluorescence labelling. The OI-RD intensities not only depend on the protein structure, but also vary with the protein concentration. The results indicate that this method should have potential applications in detection of biochemical processes.     

Investigation of Chlorophyll Protein 43 and 47 Denaturation by Terahertz Time-Domain Spectroscopy

We demonstrate the applications of terahertz time-domain spectroscopy to distinguish conformation changes of the chlorophyll proteins CP43 and CP47 induced by the treatment of guanidine hydrochloride, light irradiation and heating. It is indicated that THz transmission spectroscopy can be used for monitoring protein denaturation and associated conformation change processes in a feasible and effective way.     

Calculation of Vibrational Energy-Spectra of α-Helical Protein Molecules and Its Properties

The quantum vibrational energy-spectra of amide-Is in alpha-protein molecules are calculated by using the discretely nonlinear Schrodinger equation and physical parameters appropriate to the systems on the basis of theory of bio-energy transport. The numerical results for the energy-spectra are basically consistent with the experimental values obtained by the infrared absorption and Raman scattering and emission-spectra of infrared lights of person's hand-fingers. Utilizing the energy-spectra we explain the laser-Raman spectrum from metabolically active E. Coli. and give some features of the infrared absorption of the protein molecules.     

Properties of Soliton-Transported Bio-energy in α-Helix Protein Molecules with Three Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of α-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the α-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

Single Molecule Fluorescence of Native and Refolded Peridinin–Chlorophyll–Protein Complexes

Single molecule spectroscopy was applied to study the optical properties of native and refolded peridinin-chlorophyll-protein (PCP) complexes. The native system is a trimer with six chlorophyll a (Chl a) molecules, while the refolded one contains two Chl a and resembles structurally and spectroscopically the PCP monomer. The fluorescence emission of single PCP complexes strongly broadens with increasing excitation power. Simultaneously, the distribution of fluorescence maximum frequencies is also broadened. These spectral changes are attributed to photoinduced conformational changes of the protein that influence the fluorescence of embedded chromophores. Comparison of fluorescence intensities measured for PCP complexes in two different solvents indicates that the native PCP trimers are preserved in EDTA Tris buffer, while in PVA polymer matrix only monomers are stable.