Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work

2016 ◽  
Vol 37 (31) ◽  
pp. 2734-2742 ◽  
Author(s):  
Son Tung Ngo ◽  
Huynh Minh Hung ◽  
Minh Tho Nguyen
Keyword(s):  
Accurate Determination ◽  
Binding Affinities ◽  
Relative Binding ◽  
Hiv 1 ◽  
Non Equilibrium

A Reference Scale of Cucurbit[7]uril Binding Affinities

2021 ◽  
Author(s):  
Mohammad A. Alnajjar ◽  
Werner M Nau ◽  
Andreas Hennig
Keyword(s):  
Accurate Determination ◽  
Binding Affinities ◽  
High Binding ◽  
Reference Scale ◽  
Direct Binding ◽  
Guest Chemistry

The accurate determination of ultra-high binding affinities in supramolecular host-guest chemistry is a challenging endeavour because direct binding titrations are generally limited to affinities <106 M-1 due to sensitivity constraints...

scholarly journals Determination of binding affinities of retinoids to retinoic acid-binding protein and serum albumin

1978 ◽  
Vol 171 (3) ◽  
pp. 711-717 ◽  
Author(s):  
Brahma P. Sani ◽  
Belinda C. Titus ◽  
Chandra K. Banerjee
Keyword(s):  
Retinoic Acid ◽  
Serum Albumin ◽  
Binding Affinity ◽  
Binding Protein ◽  
Side Chain ◽  
Binding Affinities ◽  
Acid Binding Protein ◽  
Relative Binding ◽  
Biological Potency

Binding affinities of retinoic acid and its synthetic analogues to intracellular retinoic acid-binding protein, which is a possible candidate for mediating their biological function, and to serum albumin, the plasma transport protein, were evaluated. A quantitative method involving elimination of interfering serum albumin by immunoprecipitation was developed to measure the binding efficiency of these retinoids, some of which are active in modifying epithelial differentiation and preventing tumorigenesis. Two cyclopentenyl analogues of retinoic acid and 13-cis-retinoic acid showed, like retinoic acid, a binding efficiency of 100% for the cellular binding protein. With the phenyl, dichlorophenyl and trimethylmethoxyphenyl analogues of retinoic acid, the binding efficiency increased as the substituents on the aromatic ring increased; thus the trimethylmethoxyphenyl analogue binds almost as efficiently as retinoic acid itself. However, the trimethylmethoxyphenyl analogue with a sulphur atom on the side chain has a much decreased binding affinity. The correlation noticed between the binding efficiency of these retinoids and their biological activity in differentiation and/or in the control of tumorigenesis particularly enhances the confidence in the present method of determining the relative binding efficiencies. None of the vitamins, hormones and cofactors tested, showed appreciable affinity for the retinoic acid-binding site. Studies on binding of retinoic acid and its analogues to serum albumin indicate that no correlation exists between binding affinity for albumin and their biological potency.

Determination of relative binding affinities of labeling molecules with amino acids by using scanning tunneling microscopy

2011 ◽  
Vol 47 (38) ◽  
pp. 10638 ◽  
Author(s):  
Chenxuan Wang ◽  
Xiaobo Mao ◽  
Aihua Yang ◽  
Lin Niu ◽  
Shengnan Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Scanning Tunneling Microscopy ◽  
Scanning Tunneling ◽  
Binding Affinities ◽  
Tunneling Microscopy ◽  
Relative Binding

Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease

1991 ◽  
Vol 34 (8) ◽  
pp. 2654-2659 ◽  
Author(s):  
David M. Ferguson ◽  
Randall J. Radmer ◽  
Peter A. Kollman
Keyword(s):  
Peptide Inhibitors ◽  
Free Energies ◽  
Relative Binding ◽  
Hiv 1 ◽  
Binding Free Energies

A quantitative approach to inner shell losses

1978 ◽  
Vol 36 (1) ◽  
pp. 526-527 ◽  
Author(s):  
R.D. Leapman ◽  
P. Rez ◽  
D.F. Mayers
Keyword(s):  
Energy Transfer ◽  
Cross Section ◽  
Cross Sections ◽  
Accurate Determination ◽  
Background Intensity ◽  
Core Excitation ◽  
Quantitative Basis ◽  
Cross Section Differential ◽  
Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

Fast calibration of CBED patterns for quantitative analysis

1993 ◽  
Vol 51 ◽  
pp. 674-675
Author(s):  
M.A. Gribelyuk ◽  
M. Rühle
Keyword(s):  
Reciprocal Lattice ◽  
Accurate Determination ◽  
Incident Beam ◽  
Crystal Thickness ◽  
Structure Model ◽  
Beam Direction ◽  
Transmitted Beam ◽  
Reciprocal Vector ◽  
On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

Computer-Assisted High-Re Solution TEM

1990 ◽  
Vol 48 (1) ◽  
pp. 162-163
Author(s):  
F.A. Ponce ◽  
H. Hikashi
Keyword(s):  
Signal To Noise Ratio ◽  
Accurate Determination ◽  
Computer Software ◽  
Video Camera ◽  
Image Contrast ◽  
Objective Lens ◽  
Computer Assisted ◽  
Optical Parameters ◽  
Astigmatism Correction

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.

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