Embedding method for conductance studies of large molecules

2006 ◽  
pp. 509-533
Author(s):  
Owen R. Davies ◽  
John E. Inglesfield
Keyword(s):  
Embedding Method ◽  
Large Molecules

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

Directional observation on lipid of male nectary of Lindera megaphylla hemsl. by the rapid embedding method with polyethylene glycol (PEG)

1990 ◽  
Vol 48 (3) ◽  
pp. 718-719
Author(s):  
Dai Dalin ◽  
Guo Jianmin
Keyword(s):  
Electron Microscope ◽  
Polyethylene Glycol ◽  
Chemical Reaction ◽  
Traditional Method ◽  
Osmium Tetroxide ◽  
Unsaturated Lipid ◽  
Embedding Method ◽  
Long Period ◽  
New Methods

Lipid cytochemistry has not yet advanced far at the EM level. A major problem has been the loss of lipid during dehydration and embedding. Although the adoption of glutaraldehyde and osmium tetroxide accelerate the chemical reaction of lipid and osmium tetroxide can react on the double bouds of unsaturated lipid to from the osmium black, osmium tetroxide can be reduced in saturated lipid and subsequently some of unsaturated lipid are lost during dehydration. In order to reduce the loss of lipid by traditional method, some researchers adopted a few new methods, such as the change of embedding procedure and the adoption of new embedding media, to solve the problem. In a sense, these new methods are effective. They, however, usually require a long period of preparation. In this paper, we do research on the fiora nectary strucure of lauraceae by the rapid-embedding method wwith PEG under electron microscope and attempt to find a better method to solve the problem mentioned above.

HES 200/0.5 Is not HES 200/0.5

1995 ◽  
Vol 74 (06) ◽  
pp. 1452-1456 ◽  
Author(s):  
Johannes Treib ◽  
Anton Haass ◽  
Gerhard Pindur ◽  
Ulrich T Seyfert ◽  
Wolfgang Treib ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Hydroxyethyl Starch ◽  
Clinical Relevance ◽  
Dilution Effect ◽  
Repeated Administration ◽  
Plasma Viscosity ◽  
Degree Of Substitution ◽  
Pronounced Increase ◽  
Large Molecules ◽  
Mean Molecular Weight

SummaryThe plasma clearance of hydroxyethyl starch (HES) depends on the initial molecular weight and the degree of substitution. So far, little attention has been paid to the clinical relevance of the C2/C6 substitution ratio of hydroxyethyl starch.10 patients with cerebrovascular circulatory disturbance received hemodilution therapy for 10 days, consisting of 10% HES 200/0.5 (mean molecular weight 200 kD, degree of substitution 0.5) with a C2/C6 ratio of 13.4. A second group of 10 patients received a starch solution with identical initial molecular weight and degree of substitution but with a C2/C6 ratio of 5.7.After the administration of a single dose, no significant differences between the two groups were observed. After repeated administration, significant differences could be detected in hemorheology, coagulation and elimination (p<0.01). The larger C2/C6 ratio led to a higher intravascular mean molecular weight (95 vs. 84 kD), which in turn led to a higher increase in serum concentration during the therapy (14.7 vs.8.6 mg/ml). Hematocrit was lowered more (-30,5 vs. -23,5%) and plasma viscosity was increased more. There was also a more pronounced increase in partial thromboplastin time (+30% vs. +13%) and a factor of 2 larger decrease of factor VIII/von Willebrand factor-complex (p <0.01), which exceeded the dilution effect.The higher C2/C6 ratio of HES 200/0.5/13.4 slows down enzymatic degradation. After repeated administration of this starch, large molecules accumulate which are inefficiently degraded. The same effect has been observed after therapy with highly-substituted HES. This accumulation of large molecules leads to a beneficial longer lasting volume effect. The disadvantages include an increase in plasma viscosity and coagulation disturbances, which cannot be explained with the respective dilution effect alone. For these reasons, the C2/C6 ratio is of clinical relevance and should be included in the product labeling in the future.

Investigation of Information Embedding Method in Pattern by Artificial Fiber Pattern

2018 ◽  
Vol 138 (4) ◽  
pp. 435-440
Author(s):  
Wakana Tomita ◽  
Naoya Noguchi ◽  
Kitahiro Kaneda ◽  
Keiichi Iwamura ◽  
Isao Echizen
Keyword(s):  
Embedding Method ◽  
Information Embedding

On Wafer Noise Figure De-Embedding Method for CMOS Differential LNA

2020 ◽  
Vol E103.C (7) ◽  
pp. 335-340
Author(s):  
Maizan MUHAMAD ◽  
Norhayati SOIN ◽  
Harikrishnan RAMIAH
Keyword(s):  
Noise Figure ◽  
Embedding Method

A Multi-Layer Approach to the Equation of Motion Coupled-Cluster Method for the Electron Affinity

2020 ◽  
Author(s):  
Soumi Haldar ◽  
Achintya Kumar Dutta
Keyword(s):  
Electron Affinity ◽  
Electron Attachment ◽  
Equation Of Motion ◽  
Cluster Method ◽  
Coupled Cluster ◽  
Coupled Cluster Method ◽  
Large Molecules ◽  
Layer Method ◽  
Speed Up ◽  
Attachment Process

We have presented a multi-layer implementation of the equation of motion coupled-cluster method for the electron affinity, based on local and pair natural orbitals. The method gives consistent accuracy for both localized and delocalized anionic states. It results in many fold speedup in computational timing as compared to the canonical and DLPNO based implementation of the EA-EOM-CCSD method. We have also developed an explicit fragment-based approach which can lead to even higher speed-up with little loss in accuracy. The multi-layer method can be used to treat the environmental effect of both bonded and non-bonded nature on the electron attachment process in large molecules.<br>

CLB18: A New Structural Database with Unusual Carbon–Carbon Long Bonds

2020 ◽  
Author(s):  
Pierpaolo Morgante ◽  
Roberto Peverati
Keyword(s):  
Transition Metal Complexes ◽  
Low Cost ◽  
Geometry Optimization ◽  
Structure Calculation ◽  
Unique Property ◽  
Spin States ◽  
Calculation Methods ◽  
Large Molecules ◽  
Barrier Heights ◽  
Structural Database

<div><div><div><p>In this Letter, we introduce a new database called carbon long bond 18 (CLB18), composed of 18 structures with one long C–C bond. We use this new database to evaluate the performance of several low-cost methods commonly used for geometry optimization of medium and large molecules. We found that the long bonds in CLB18 are electronically different from those found in barrier heights databases. We also report the unexpected correlation between the results of CLB18 and those of the energetics of spin states in transition-metal complexes. Given this unique property, CLB18 can be a useful tool for assessing existing electronic structure calculation methods and developing new ones.</p></div></div></div>

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

STUDY ON THE EFFECT OF THE CATGUT-EMBEDDING METHOD COMBINING WITH HERBAL MEDICINE ON THE TREATMENT OF SCIATICA BY WIND-COLD-DAMP ARTHRALGIA

2014 ◽  
pp. 206-215
Author(s):  
Huu Tham Nguyen ◽  
Thi Tan Nguyen
Keyword(s):  
Herbal Medicine ◽  
Traditional Medicine ◽  
Clinical Characteristics ◽  
Day Treatment ◽  
Patient Treatment ◽  
Control Group ◽  
Controlled Trials ◽  
Study Group ◽  
Moderate Pain ◽  
Embedding Method

Objectives: To investigate clinical characteristics of patients with sciatica in Traditional Medicine Hospital in Thua Thien Hue province; To evaluate the effectiveness of the catgut-embedding method combining with herbal medicine on the treatment of sciatica by wind-cold-damp arthralgia. Subjects and Methods: Patients diagnosed with sciatica by wind-cold-damp arthralgia in-patient treatment in Traditional Medicine Hospital in Thua Thien Hue province. Methods: Clinical and controlled trials, a survey of 72 patients, which were divided into 2 groups: The study group: 36 patients: receiving treatment by catgut-embedding and herbal medicine; The control group: 36 patients: only use herbal medicine. 28-day treatment period. Patients were assessed at admission (T0), after 14 days (T14), after 28 days of treatment (T28). Results: After 28 days of treatment: no severity both 2 groups. The study group fell to 8.3% moderate pain, mostly mild pain (91.7%); the control group was 44.4% moderate pain, mild 55.6%.The catgut-embedding method does not cause any side effects. Key words: catgut-embedding method, sciatica by wind-cold-damp arthralgia

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