Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.     

Effect of some factors on the energy band structure of proteins

The effects of four factors (different side chains, side-chain disorder, conformational change, and ions and water) on the energy band structures of proteins have been investigated with the aid of the CNDO/2 crystal orbital method. The results indicate that these factors are very important. The consequences of these effects on the semiconductive properties of proteins are discussed.     

π -Type and σ -type cation- π complexes of atomic cations

MP2/6-31+G* calculations were performed on the cation- complexes of ethylene, cyclobutadiene and benzene with a number of atomic cations. It was found that except B⁺ all the atomic cations form -type cation- complexes with ethylene. On the other hand, with cyclobutadiene Li⁺, N⁺, Na⁺, P⁺ and K⁺ form -type complexes, whereas H⁺, F⁺, and Cl⁺ form covalent -type complexes. With benzene Li⁺, B⁺, Na⁺, Al⁺, and K⁺ form -type complexes whereas H⁺, F⁺, and Cl⁺ form -type complexes. It was concluded that the driving force to form the -type complex is chemical bonding, and that for metal cations to form -type complexes is non-covalent interaction.     

Reversible replication between ordered mesoporous silica and mesoporous carbon

Highly ordered mesoporous silica can be regenerated from a mesoporous carbon CMK-3 that is a negative replica of mesoporous silica SBA-15, indicating reversible replication between carbon and inorganic materials.     

Detection of a biomarker for Alzheimer's disease from synthetic and clinical samples using a nanoscale optical biosensor

A nanoscale optical biosensor based on localized surface plasmon resonance (LSPR) spectroscopy has been developed to monitor the interaction between the antigen, amyloid-beta derived diffusible ligands (ADDLs), and specific anti-ADDL antibodies. Using the sandwich assay format, this nanosensor provides quantitative binding information for both antigen and second antibody detection that permits the determination of ADDL concentration and offers the unique analysis of the aggregation mechanisms of this putative Alzheimer's disease pathogen at physiologically relevant monomer concentrations. Monitoring the LSPR-induced shifts from both ADDLs and a second polyclonal anti-ADDL antibody as a function of ADDL concentration reveals two ADDL epitopes that have binding constants to the specific anti-ADDL antibodies of 7.3 x 10(12) M(-1) and 9.5 x 10(8) M(-1). The analysis of human brain extract and cerebrospinal fluid samples from control and Alzheimer's disease patients reveals that the LSPR nanosensor provides new information relevant to the understanding and possible diagnosis of Alzheimer's disease.     

Adsorption of 1,10-phenanthroline within a dodecanethiol monolayer: an approach to a switchable electrode surface

A simple method was used to prepare a "switchable" electrode surface by using self-assembled monolayers of dodecanethiol on a gold electrode. The dodecane-modified electrode was electrochemically inactive until the monolayer was soaked in solutions of 1,10-phenanthroline or 2,2'-bipyridine. The electroactive form of the electrode could be reverted back to the nonelectroactive form by rinsing the electrode. Surface IR results showed that both dodecanethiol and 1,10-phenanthroline exist in the mixed monolayer.     

A New Approach to α—Bromochalcones

α-Bromo benzolymethylene triphenylphosphorane 3 has been synthesized by the reaction of benzoylmethylene triphenylphosphorane 1 with N-bromosuccinimide in the yield of 87% and can react with aromatic aldehydes 4 to give α-bromochalcones 5 in good yields.     

Co-C bond dissociation energy and reaction volume change of 2',5'-dideoxyadenosylcobalamin studied by laser-induced time-resolved photoacoustic calorimetry

Time resolved photoacoustic calorimetry (PAC) was applied to a study of the photolysis of a coenzyme B(12) analog 2',5'-dideoxyadenosylcobalamin, which lacks an -OH group at the 2' position of ribofuranose ring. In aqueous solution, we report for the first time the quantum yield Phi(d) (0.25+/-0.02), Co-C bond dissociation energy (BDE; 31.8+/-2.5 kcal mol(-1)) and reaction volume change deltaV(R) (6.5+/-0.5 ml mol(-1)) due to conformation changes of the corrin ring and its side chains accompanying the cleavage of the Co-C bond. These values for the analog are very similar to those for the natural cofactor. Based our results and previous studies, a possible explanation for the similarity in their structure and properties versus the large difference in their enzymatic activity is discussed.     

Remote substituent effects on bond dissociation energies of para-substituted aromatic silanes

UB3LYP/6-31G(d) and ROMP2/6-311++G(d,2p) methods were used to calculate the Si-X bond dissociation energies (BDEs) of a number of para-substituted aromatic silanes (4-Y-C(6)H(4)-SiH(2)X, where X = H, F, Cl, or Li). It was found that the substituent effect on the Si-H BDE of 4-Y-C(6)H(4)-SiH(3) was small, as the slope (rho(+)()) of the BDE- regression was only 0.09 kJ/mol. In comparison, the substituent effect on the Si-F BDE of 4-Y-C(6)H(4)-SiH(2)F was much stronger, whose rho(+ )()value was -2.34 kJ/mol. The substituent effect on the Si-Cl BDE of 4-Y-C(6)H(4)-SiH(2)Cl was also found to be strong with a rho(+)() value of -1.70 kJ/mol. However, the substituent effect on the Si-Li BDE of 4-Y-C(6)H(4)-SiH(2)Li was found to have a large and positive slope (+9.12 kJ/mol) against. The origin of the above remarkably different substituent effects on the Si-X BDEs was found to be associated with the ability of the substituent to stabilize or destabilize the starting material (4-Y-C(6)H(4)-SiH(2)X) as well as the product (4-Y-C(6)H(4)-SiH(2)* radical) of the homolysis. Therefore, the direction and magnitude of the effects of Y-substituents on the Z-X BDEs in compounds such as 4-YC(6)H(4)Z-X should have some important dependence on the polarity of the Z-X bond undergoing homolysis. This conclusion was in agreement with that from earlier studies (for example, J. Am. Chem. Soc. 1991, 113, 9363). However, it indicated that the proposal from a recent work (J. Am. Chem. Soc. 2001, 123, 5518) was unfortunately not justified.