Structure-mechanics statistical learning uncovers mechanical relay in proteins

A protein''s adaptive response to its substrates is one of the key questions driving molecular physics and physical chemistry. This work employs the recently developed structure-mechanics statistical learning method to establish a mechanical perspective. Specifically, by mapping all-atom molecular dynamics simulations onto the spring parameters of a backbone-side-chain elastic network model, the chemical moiety specific force constants (or mechanical rigidity) are used to assemble the rigidity graph, which is the matrix of inter-residue coupling strength. Using the S1A protease and the PDZ3 signaling domain as examples, chains of spatially contiguous residues are found to exhibit prominent changes in their mechanical rigidity upon substrate binding or dissociation. Such a mechanical-relay picture thus provides a mechanistic underpinning for conformational changes, long-range communication, and inter-domain allostery in both proteins, where the responsive mechanical hotspots are mostly residues having important biological functions or significant mutation sensitivity.

Protein residues exhibit specific routes of mechanical relay as the adaptive responses to substrate binding or dissociation. On such physically contiguous connections, residues experience prominent changes in their coupling strengths.     

Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems

We have simulated pure liquid butane, methanol, and hydrated alanine polypeptide with the Monte Carlo technique using three kinds of random number generators (RNG's)—the standard Linear Congruential Generator (LCG), a modification of the LCG with additional randomization used in the BOSS software, and the “Mersenne Twister” generator by Matsumoto and Nishimura. While using the latter two RNG's leads to reasonably similar physical features, the LCG produces significant different results. For the pure fluids, a noticeable expansion occurs. Using the original LCG on butane yields, a molecular volume of 171.4 ų per molecule compared to about 163.6–163.9 ų for the other two generators, a deviation of about 5%. For methanol, the LCG produces an average volume of 86.3 ų per molecule, which is about 24% higher than the 68.8–70.2 ų obtained with the RNG's in BOSS and the generator by Matsumoto and Nishimura. In case of the hydrated tridecaalanine peptide, the volume and energy tend to be noticeably greater with the LCG than with the BOSS (modified LCG) RNG's. For the simulated hydrated extended conformation of tridecaalanine, the difference in volume reached about 87%. The uniformity and periodicity of the generators do not seem to play the crucial role in these phenomena. We conclude that, it is important to test a RNG's by modeling a system such as the pure liquid methanol with a well‐established force field before routinely employing it in Monte Carlo simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Visual spatial memory is enhanced in female rats (but inhibited in males) by dietary soy phytoestrogens

Background  

In learning and memory tasks, requiring visual spatial memory (VSM), males exhibit superior performance to females (a difference attributed to the hormonal influence of estrogen). This study examined the influence of phytoestrogens (estrogen-like plant compounds) on VSM, utilizing radial arm-maze methods to examine varying aspects of memory. Additionally, brain phytoestrogen, calbindin (CALB), and cyclooxygenase-2 (COX-2) levels were determined.     

Hydroxyl Substituent Chemical Shift (SCS) Effects in Alcohols: The 17O NMR of Diols

The ¹⁷O NMR spectra for a series of saturated diols were investigated. From these studies both hydroxyl induced substituent chemical shift (SCS) effects of hydroxyl oxygen ¹⁷O NMR chemical shifts were determined. In addition, linear correlations between the ¹⁷O chemical shift of the hydroxyl oxygen (ROH) and the ¹³C chemical shift for the methyl group in the corresponding hydrocarbon (RCH₃) were obtained.

     

Formation of a samarium alkoxide–aryloxide complex containing a novel butterfly framework: X-ray crystal structures of Sm4(μ3-O-i-Pr)3(μ2-O-i-Pr)4(O-i-Pr)2(O-2,6-i-Pr2C6H3)3(THF) and [Ti(O-i-Pr)2(O-2,6-i-Pr2C6H3) (μ-O-i-Pr)]2

Reaction of a 1:1 mixture of Sm[N(SiMe₃)₂]₃ and Ti(O-i-Pr)₄ with three equivalents of 2,6-di-iso-propylphenol, followed by crystallization from hexane/THF, leads to isolation of the tetranuclear samarium alkoxide Sm₄(₃-O-i-Pr)₃(₂-O-i-Pr)₄(O-i-Pr)₂(O-2,6-i-Pr₂C₆H₃)₃(THF) (1), in addition to the dimeric titanium alkoxide [Ti(O-i-Pr)₂(O-2,6-i-Pr₂C₆H₃)(-O-i-Pr)]₂ (2). 1 crystallizes in the space group while 2 crystallizes in space group P2₁/c. Cell parameters for 1: a = 15.928(6), b = 17.677(7), c = 18.99(1) Å, = 113.24(3), = 94.99(4), = 109.59(2)°, V = 4477(4) ų, D _calc = 1.350 Mg/m³, and Z = 2. Cell parameters for 2: a = 25.336(2), b = 12.082(1), c = 15.570(2) Å, = 96.510(8)°, V = 4735.4(8) ų, D _calc = 1.129 mg/m³, and Z = 4.     

The application of homotopy analysis method to solve nonlinear differential equation governing Jeffery–Hamel flow

In this paper Jeffery–Hamel flow has been studied and its nonlinear ordinary differential equation has been solved through homotopy analysis method (HAM). The obtained solution in comparison with the numerical ones represents a remarkable accuracy. The results also indicate that HAM can provide us with a convenient way to control and adjust the convergence region.     

Neuromodulation by soy diets or equol: Anti-depressive &; anti-obesity-like influences,age- &; hormone-dependent effects

Background  

Soy-derived isoflavones potentially protect against obesity and depression. In five different studies we examined the influence of soy-containing diets or equol injections on depression, serotonin levels, body weight gain (BW) and white adipose tissue (WAT) deposition in female Long-Evans rats at various stages of life [rats were intact, ovariectomized or experienced natural ovarian failure (NOF)].     

Influence of ionic-liquid incubation temperature on changes in cellulose structure,biomass composition,and enzymatic digestibility

Varying ionic liquid, 1-ethyl 3-methyl imidazolium acetate, pretreatment incubation temperature on lignocellulosic biomass substrates, corn stover, switchgrass and poplar, can have dramatic effects on the enzymatic digestibility of the resultant regenerated biomass. In order to delineate the chemical and physical changes resulting from the pretreatment process and correlate changes with enzymatic digestibility, X-ray powder and fiber diffraction, ¹³C cross polarization/magic angle spinning nuclear magnetic resonance spectroscopy, and compositional analysis was completed on poplar, corn stover and switchgrass samples. Optimal pretreatment incubation temperatures were most closely associated with the retention of amorphous substrates upon drying of regenerated biomass. Maximal glucan to glucose conversion for 24 h enzyme hydrolysis was observed for corn stover, switchgrass and poplar at ionic liquid incubation temperatures of 100, 110 and 120 °C, respectively. We hypothesize that effective pretreatment temperatures must attain lignin redistribution and retention of xylan for optimal enzyme digestibility.