Fluctuation and linkage relations in macromolecular solution

It is shown in the appendix that the derivatives of the excess free energy of a macromolecule in solution, with respect to the activities of other solution components, lead to fluctuation and linkage relations among these other components. Solution fluctuation theory is used, but it is specialized to the fluctuations and correlations associated with the presence of a macromolecule, and is developed with a modified ensemble. The relations of the appendix are used to analyze the interaction of two solution components, A and B, with the macromolecule and with one another. Three cases are considered: (1) A and B are ligands that bind stoichiometrically to the macromolecule. This case reduces to Wyman's binding polynomial analysis. (2) A and B are two substances at high concentration that interact selectively with the macromolecule. (3) A is a species that binds stoichiometrically to the macromolecule, while B is a component at high concentration that interacts weakly with the macromolecule.     

An electrophoretic device concentrating charged macromolecules to a predetermined final solution volume

An apparatus for electrophoretic concentration of charged macromolecules to a predetermined final solution volume has been developed. The concentration process has a yield of near 100%, which implies that it is possible to predetermine the final macromolecule concentration as well. Both the final macromolecule solution volume and concentration are nearly independent of the electrophoresis time when it exceeds a certain minimum value. The electric field strength across the boundary containing the concentrated macromolecule solution is very low. This considerably reduces macromolecule aggregation, adsorption, and denaturation at this boundary compared to conventional electrophoretic concentrator designs. Both one-stage and two-stage versions of the apparatus have been developed. The one-stage version easily yields a 10-fold and the two-stage version a 50-fold concentration of the macromolecules. Typical macromolecule solution start volumes are 20-50 ml.     

Hydroxycinnamic acids are ester-linked directly to glucosyl moieties within the lignan macromolecule from flaxseed hulls

In flaxseed hulls, lignans are present in an oligomeric structure. Secoisolariciresinol diglucoside (SDG), ester-linked to hydroxy-methyl-glutaric acid (HMGA), forms the backbone of this lignan macromolecule. The hydroxycinnamic acids p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) are also part of the lignan macromolecule. However, their position and type of linkage are still unknown. The aim of this study was to investigate how CouAG and FeAG are linked within the lignan macromolecule from flaxseed hulls. Fragments of the lignan macromolecule were obtained by partial saponification. After isolation of the fragments by preparative RP-HPLC, several key structures were identified by MS and NMR. Within the lignan macromolecule, CouAG is attached to the C-6 position of a glucosyl moiety of SDG. FeA is linked to the C-2 position of a glucosyl moiety of SDG. FeAG is ester-linked within the lignan macromolecule with its carboxyl group, but it remains unclear whether FeAG links to the C-2 or C-6 position of SDG. Attachment of HMGA to the glucosyl moiety of CouAG or FeAG was not observed. The results clearly show that within the lignan macromolecule, the hydroxycinnamic acids are linked directly via an ester bond to the glucosyl moiety of SDG.     

有机无机改性钾肥的结构特征及其增效机理

应用有机、无机(矿物)控释材料对化学钾肥(KCl)进行化学改性,制备出长效有机、无机(矿物)改性钾肥。有机、无机(矿物)改性钾肥具有长效性,盆栽试验表明,改性钾肥对第二作玉米幼苗具有显著的增产作用。X射线衍射表明,改性钾肥的结构变化与改性材料层间域的性质、改性材料与化学钾肥的适当比例及改性反应的物理化学条件有关。化学氯化钾肥的红外光谱较弱,且有一高分子包膜层。经有机、无机改性后,高分子包膜层被破坏,这层包膜层的破坏并没有降低改性钾肥钾的有效性,相反,有机、无机(矿物)的非包膜控释作用比高分子包膜层更具长效性。     

In vivo brain macromolecule signals in healthy and glioblastoma mouse models: 1H magnetic resonance spectroscopy,post‐processing and metabolite quantification at 14.1 T

In ¹H magnetic resonance spectroscopy, macromolecule signals underlay metabolite signals, and knowing their contribution is necessary for reliable metabolite quantification. When macromolecule signals are measured using an inversion‐recovery pulse sequence, special care needs to be taken to correctly remove residual metabolite signals to obtain a pure macromolecule spectrum. Furthermore, since a single spectrum is commonly used for quantification in multiple experiments, the impact of potential macromolecule signal variability, because of regional differences or pathologies, on metabolite quantification has to be assessed. In this study, we introduced a novel method to post‐process measured macromolecule signals that offers a flexible and robust way of removing residual metabolite signals. This method was applied to investigate regional differences in the mouse brain macromolecule signals that may affect metabolite quantification when not taken into account. However, since no significant differences in metabolite quantification were detected, it was concluded that a single macromolecule spectrum can be generally used for the quantification of healthy mouse brain spectra. Alternatively, the study of a mouse model of human glioma showed several alterations of the macromolecule spectrum, including, but not limited to, increased mobile lipid signals, which had to be taken into account to avoid significant metabolite quantification errors.     

The flavonoid herbacetin diglucoside as a constituent of the lignan macromolecule from flaxseed hulls

Lignans in flaxseed are known to be part of a macromolecule in which they are connected through the linker-molecule hydroxy-methyl-glutaric acid (HMGA). In this study, the lignan macromolecule was extracted from flaxseed hulls and degraded to its monomeric constituents by complete saponification. Besides secoisolariciresinol diglucoside (SDG), the phenolic compounds p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) were isolated, which was expected based on indications from the literature. Also the flavonoid herbacetin diglucoside (HDG) was found. The presence of HDG was confirmed by NMR following preparative RP-HPLC purification. Also the presence of the three other constituents (CouAG, FeAG and SDG) was confirmed by NMR. To prove that HDG is a substructure of the lignan macromolecule, the macromolecule was fragmented by partial saponification. A fragment consisting of HDG and HMGA was indicated. This fragment was isolated by preparative RP-HPLC and its identity was confirmed by NMR. It is concluded that the flavonoid HDG is a substructure of the lignan macromolecule from flaxseed hulls and that it is incorporated in the macromolecule via the same linker-molecule as SDG.     

大分子的吸入治疗

随着重组DNA技术和分子生物学的发展,以蛋白质和多肽为主的大分子成为一类新型药物,并越来越受到重视,新兴的基因治疗技术使得核酸大分子也有可能成为药物。目前,绝大部分大分子药物都是通过注射途径给药,病人在医院注射费用昂贵且不方便,因而许多注射替代给药途径成为研究热门,通过肺部吸入给药就是一种很有吸引力的非侵入性给药途径。本介绍了肺吸收大分子的可能机制和大分吸入治疗的临床与基础研究以及面临的问题。     

Combined action of static and alternating magnetic fields on ion motion in a macromolecule: Theoretical aspects

This is an attempt to solve the energetic problem of the primary detection of weak parallel static (DC) and alternating (AC) extremely low frequency (ELF) magnetic fields. We studied the equations of motion for an ion situated inside a macromolecule under the influence of these fields. The main concern is with the magnetic field influence on thermal motion of the ion in the macromolecule. The resonance effects are revealed at discrete frequencies of the ion thermal oscillations determined by the DC field magnitude and the AC field frequency. These phenomena result from the Larmor precession of the ion thermal motion. When the DC field or, to a greater extent, the combined DC and AC fields with the specific frequencies are turned on or cut off, changes occur in the energy of the ion thermal motion. If, inside the macromolecule, the ion is sufficiently protected against immediate impacts of particles of the medium surrounding the macromolecule, these changes may be enough to trigger alteration in the quantum state of the macromolecule. Bioelectromagnetics 19:279–292, 1998. © 1998 Wiley-Liss, Inc.     

The chain length of lignan macromolecule from flaxseed hulls is determined by the incorporation of coumaric acid glucosides and ferulic acid glucosides

Lignan macromolecule from flaxseed hulls is composed of secoisolariciresinol diglucoside (SDG) and herbacetin diglucoside (HDG) moieties ester-linked by 3-hydroxy-3-methylglutaric acid (HMGA), and of p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) moieties ester-linked directly to SDG. The linker molecule HMGA was found to account for 11% (w/w) of the lignan macromolecule. Based on the extinction coefficients and RP-HPLC data, it was determined that SDG contributes for 62.0% (w/w) to the lignan macromolecule, while CouAG, FeAG, and HDG contribute for 12.2, 9.0, and 5.7% (w/w), respectively.Analysis of fractions of lignan macromolecule showed that the higher the molecular mass, the higher the proportion of SDG was. An inverse relation between the molecular mass and the proportion (%) CouAG + FeAG was found. Together with the structural information of oligomers of lignan macromolecule obtained after partial saponification, it is hypothesized that the amount of CouAG + FeAG present during biosynthesis determines the chain length of lignan macromolecule.Furthermore, the chain length was estimated from a model describing lignan macromolecule based on structural and compositional data. The average chain length of the lignan macromolceule was calculated to be three SDG moieties with CouAG or FeAG at each of the terminal positions, with a variation between one and seven SDG moieties.     

DC和AC磁场混合作用下的离子运动

本文研讨了在微弱ＤＣ磁场和频率非常低的ＡＣ磁场并行作用下，位于大分子内部的离子运动情况。主要焦点是大分子中磁场对离子热运动的影响，通过一些离散频率的分析揭示了热运动的共振效应。指出当ＤＣ和ＡＣ磁场施加或切断时离子热运动能量将发生变化，如果大分子周围的媒介质的粒子能充分阻止瞬间接触，就会引起大分了子量子态的变化。     

Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding

Two fundamentally different mechanisms of ligand binding are commonly encountered in biological kinetics. One mechanism is a sequential multistep reaction in which the bimolecular binding step is followed by first-order steps. The other mechanism includes the conformational transition of the macromolecule, before the ligand binding, followed by the ligand binding process to one of the conformational states. In stopped-flow kinetic studies, the reaction mechanism is established by examining the behavior of relaxation times and amplitudes as a function of the reactant concentrations. A major diagnostic tool for detecting the presence of a conformational equilibrium of the macromolecule, before the ligand binding, is the decreasing value of one of the reciprocal relaxation times with the increasing [ligand]. The sequential mechanism cannot generate this behavior for any of the relaxation times. Such dependence is intuitively understood on the basis of approximate expressions for the relaxation times that can be comprehensively derived, using the characteristic equation of the coefficient matrix and polynomial theory. Generally, however, the used approximations may not be fulfilled. On the other hand, the two kinetic mechanisms can always be distinguished, using the approach based on the combined application of pseudo-first-order conditions, with respect to the ligand and the macromolecule. The two experimental conditions differ profoundly in the extent of the effect of the ligand on the protein conformational equilibrium. In a large excess of the ligand, the conformational equilibrium of the macromolecule, before the ligand binding, is strongly affected by the binding process. However, in a large excess of the macromolecule, ligand binding does not perturb the internal equilibrium of the macromolecule. As a result, the normal mode, affected by the conformational transition, is absent in the observed relaxation process. In the case of a sequential mechanism, the number of relaxation times is not altered by different pseudo-first-order conditions. Thus, the approach provides a strong diagnostic criterion for detecting the presence of the conformational transition of the macromolecule and establishing the correct mechanism. Application of this approach is illustrated for the binding of 3'-O-(N-methylantraniloyl)-5'-diphosphate to the E. coli DnaC protein.     

Effect of the external electrostatic field on the conformation of a macromolecule containing charged groups

A method for calculating the free energy of a macromolecule containing charged groups in electrostatic field in aqueous solution was proposed. The non-electrostatic component of free energy was calculated with consideration of van der Waals interactions between uncharged parts of the macromolecule. The electrostatic component of free energy was calculated with regard for the interactions of charged groups of the macromolecule with each other and with water molecules. It was found that, depending on the strength of external electric field, the free energy of the system passes through a minimum, whereas the internal energy passes through a maximum. By minimizing the free energy, relative changes in the mean radius 'r' and the distance between the termini of the macromolecule 'h' were calculated. It was found that, at some values of field strength, both 'r' and 'h' decrease. An increase in strength led to an increase in 'r' and 'h'. The regularities observed depend on the charge of the macromolecule and the spatial redistribution of macromolecules and counterions.     

Calcium-binding protein in sieve tube exudate

A calcium-binding macromolecule, with an estimated molecular weight greater than 100,000, was detected in phloem exudate from Cucurbita maxima and related species. The macromolecule was a component of sieve tube sap, rather than a contaminant leached from cell walls or cut parenchyma cells during exudate collection. The protein nature of this macromolecule was deduced from its size, lability, susceptibility to proteolytic digestion, and by the dependence of calcium-binding activity on thiol-protecting agents. This protein is distinct from the major proteins of exudate and does not appear to be related to calmodulin.Abbreviations SDS-PAGE sodium dodecyl sulphate polyacrylamide gel electrophoresis - CBP calcium-binding protein     

Solubilization and properties of the soluble axonal cholinergic binding macromolecule

Lysolecithin has been used to solubilize the axon plasma membrane preparation from lobster walking legs. This was accomplished with complete recovery of activity of the axonal cholinergic binding macromolecule and retention of the basic properties of the membrane-bound macromolecule. Sedimentation of the soluble protein through a sucrose gradient containing [³H]nicotine enabled the separation of the axonal cholinergic binding macromolecule from acetylcholinesterase and demonstrated the apparent dissociation of the axonal cholinergic binding macromolecule in low ionic strength solutions.     

Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the lac repressor-operator system.

The association of a molecule onto a specified binding site on a large chain-like macromolecule is described in the "sliding" model, where the molecule is allowed to move along the chain in a one-dimensional diffusion which is coupled to the three-dimensional diffusion in solution. The present work extends a previous one by treating the chains more generally as coiled instead of straight. The model is applied to the lac repressor-operator association. A general expression for the rate of unspecific attachment to a chain-like macromolecule is also derived.     

204 Polymer translocation

The translocation of a single macromolecule through a protein pore or a solid-state nanopore involves three major stages: (1) approach of the macromolecule towards the pore, (2) capture/recognition of the macromolecule at the pore entrance, and (3) threading through the pore (see the Figure) (Muthukumar, 2011). All of these stages are controlled by conformational entropy of the macromolecule, charge decoration, and the geometry of the pore, hydrodynamics, and electrostatic interactions. Chief among the contributing factors are the entropic barrier presented by the pore to the penetration of the macromolecule, pore–polymer interactions, electro-osmotic flow, and the drift-diffusion of the macromolecule in electrolyte solutions. A unifying theory of these contributing factors will be described in the context of a few illustrative experimental data on DNA translocation and protein translocation through protein pores and solid-state nanopores. Future challenges to specific biological systems will be briefly discussed.     

Frequency and amplitude windows in the combined action of DC and low frequency AC magnetic fields on ion thermal motion in a macromolecule: theoretical analysis

We solved the differential equation describing combined action of DC and AC magnetic fields on thermal motion of ions in a biological macromolecule. The solution showed the occurrence of a new set of resonant peaks for ion oscillations under the influence of magnetic fields. After establishment of steady ion oscillations in the macromolecule interior that is well shielded from the action of small particles of the medium surrounding this molecule, the change in energy of ion thermal motion could be sufficient to alter the conformation state of the macromolecule. On this basis, a diversity of biological phenomena can be explained, including the appearance of the known "frequency" and "amplitude" windows, without any resort to the ideas of participation of cyclotron or parametric resonances in these effects.     

Phasing macromolecular structures with UV-induced structural changes

Experimental phasing of macromolecular crystal structures relies on the accurate measurement of two or more sets of reflections from isomorphous crystals, where the scattering power of a few atoms is different for each set. Recently, it was demonstrated that X-ray-induced intensity differences can also contain phasing information, exploiting specific structural changes characteristic of X-ray damage. This method (radiation damage-induced phasing; RIP) has the advantage that it can be performed on a single crystal of the native macromolecule. However, a drawback is that X-rays introduce many small changes to both solvent and macromolecule. In this study, ultraviolet (UV) radiation has been used to induce specific changes in the macromolecule alone, leading to a larger contrast between radiation-susceptible and nonsusceptible sites. Unlike X-ray RIP, UV RIP does not require the use of a synchrotron. The method has been demonstrated for a series of macromolecules.     

Kinetics of low-frequency excitations in globular macromolecules

The kinetics of low-frequency rotational-vibrational excitations of globular macromolecules is studied. The macromolecule is modelled by a viscous liquid-like deformable body with the thermal motion being generated by the stochastic motion of its surface. The collective excitations are treated in terms of dynamic variables describing the deviations of the macromolecule shape from its equilibrium spherical form. Thermal fluctuations of the variables are described using the kinetic Einstein-Smoluchowski equation. The probability density of the change of the macromolecule dynamical state is found. The Van Hove correlation function determining the spectrum of the Rayleigh scattering of Mössbauer gamma-quanta is calculated. The spectrum is found for large values of the momentum transfer at the scattering, k. The effective width of the spectrum is shown to be proportional to k ³T/, where T is the temperature and is the macromolecule viscosity.