Evolving Trends in Transition Metal-Modified Receptor Design and Function

2012 ◽  
pp. 239-259
Author(s):  
Paul A. Bertin
Keyword(s):  
Transition Metal ◽  
Receptor Design ◽  
And Function

Lithium transition metal pnictides – structural chemistry, electrochemistry, and function

2015 ◽  
Vol 35 (1) ◽  
pp. 1-24 ◽  
Author(s):  
Florian Winter ◽  
Rainer Pöttgen ◽  
Magnus Greiwe ◽  
Tom Nilges
Keyword(s):  
Solid State ◽  
Transition Metal ◽  
Crystal Structures ◽  
Chemical Bonding ◽  
Electrochemical Behavior ◽  
Solid State Nmr ◽  
Structural Chemistry ◽  
Covalently Bonded ◽  
Interesting Class ◽  
And Function

AbstractLithium-transition metal (T)-pnictides (Pn=P, As, Sb, Bi) are an interesting class of materials with greatly differing crystal structures. The transition metal and pnictide atoms build up covalently bonded networks that leave cavities or channels for the lithium atoms. Depending on the bonding of lithium to the polyanionic network, one observes mobility of the lithium atoms. The crystal chemistry, chemical bonding, 7Li solid-state NMR, and the electrochemical behavior of the pnictides are reviewed. The structural chemistry is compared with related tetrelides.

scholarly journals Comparison of different approaches to derive classical bonded force-field parameters for a transition metal cofactor: a case study for non-heme iron site of ectoine synthase

2021 ◽  
Vol 140 (8) ◽  
Author(s):  
Justyna Andrys ◽  
Johann Heider ◽  
Tomasz Borowski
Keyword(s):  
Transition Metal ◽  
Force Field ◽  
Metal Ion ◽  
Geometry Optimization ◽  
Heme Iron ◽  
Energy Structure ◽  
Test Case ◽  
Amber Force Field ◽  
Force Field Parameters ◽  
And Function

AbstractComputational investigations into the structure and function of metalloenzymes with transition metal cofactors require proper preparation of the model, which requires obtaining reliable force field parameters for the cofactor. Here, we present a test case where several methods were used to derive amber force field parameters for a bonded model of the Fe(II) cofactor of ectoine synthase. Moreover, the spin of the ground state of the cofactor was probed by DFT and post-HF methods, which consistently indicated the quintet state is lowest in energy and well separated from triplet and singlet. The performance of the obtained force field parameter sets, derived for the quintet spin state, was scrutinized and compared taking into account metrics focused on geometric features of the models as well as their energetics. The main conclusion of this study is that Hessian-based methods yield parameters which represent the geometry around the metal ion, but poorly reproduce energy variance with geometrical changes. On the other hand, the energy-based method yields parameters accurately reproducing energy-structure relationships, but with bad performance in geometry optimization. Preliminary tests show that admixing geometrical criteria to energy-based methods may allow to derive parameters with acceptable performance for both energy and geometry.

Zinc: An important cofactor in haemostasis and thrombosis

2013 ◽  
Vol 109 (03) ◽  
pp. 421-430 ◽  
Author(s):  
Trang Vu ◽  
James Fredenburgh ◽  
Jeffrey Weitz
Keyword(s):  
Platelet Aggregation ◽  
Transition Metal ◽  
Zinc Deficiency ◽  
Plasma Proteins ◽  
Structure And Function ◽  
Important Mediator ◽  
Activated Platelets ◽  
And Function

SummaryThere is mounting evidence that zinc, the second most abundant transition metal in blood, is an important mediator of haemostasis and thrombosis. Prompted by the observation that zinc deficiency is associated with bleeding and clotting abnormalities, there now is evidence that zinc serves as an effector of coagulation, anticoagulation and fibrinolysis. Zinc binds numerous plasma proteins and modulates their structure and function. Because activated platelets secrete zinc into the local microenvironment, the concentration of zinc increases in the vicinity of a thrombus. Consequently, the role of zinc varies depending on the microenvironment; a feature that endows zinc with the capacity to spatially and temporally regulate haemostasis and thrombosis. This paper reviews the mechanisms by which zinc regulates coagulation, platelet aggregation, anticoagulation and fibrinolysis and outlines how zinc serves as a ubiquitous modulator of haemostasis and thrombosis.

Synthesis, Structure, and Function of PCP Pincer Transition-Metal-Complex-Bound Norvaline Derivatives

Synlett ◽  
2013 ◽  
Vol 24 (15) ◽  
pp. 1910-1914 ◽  
Author(s):  
Hikaru Takaya ◽  
Masaharu Nakamura ◽  
Takashi Iwaya ◽  
Kazuki Ogata ◽  
Katsuhiro Isozaki ◽  
...  
Keyword(s):  
Transition Metal ◽  
Metal Complex ◽  
Transition Metal Complex ◽  
Structure And Function ◽  
Pcp Pincer ◽  
And Function

scholarly journals ChemSpaX: Exploration of Chemical Space by Automated Functionalization of Molecular Scaffold

2021 ◽  
Author(s):  
Adarsh Kalikadien ◽  
Evgeny A. Pidko ◽  
Vivek Sinha
Keyword(s):  
Transition Metal ◽  
Chemical Space ◽  
Data Driven ◽  
Molecular Scaffolds ◽  
Molecular Scaffold ◽  
Automated Generation ◽  
Design And Optimization ◽  
Screening Design ◽  
Computational Screening ◽  
And Function

Exploration of the local chemical space of molecular scaffolds by post-functionalization (PF) is a promising route to discover novel molecules with desired structure and function. PF with rationally chosen substituents based on known electronic and steric properties is a commonly used experimental and computational strategy in screening, design and optimization of catalytic scaffolds. Automated generation of reasonably accurate geometric representations of post-functionalized molecular scaffolds is highly desirable for data-driven applications. However, automated PF of transition metal (TM) complexes remains challenging. In this work a Python-based workflow, ChemSpaX, that is aimed at automating the PF of a given molecular scaffold with special emphasis on TMcomplexes, is introduced. In three representative applications of ChemSpaX by comparing with DFT and DFT-B calculations, we show that the generated structures have a reasonable quality for use in computational screening applications. Furthermore, we show thatChemSpaXgenerated geometries can be used in machine learning applications to accurately predict DFT computed HOMO-LUMO gaps for transition metal complexes.ChemSpaXis open-source and aims to bolster and democratize the efforts of the scientific community towards data-driven chemical discovery.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

The Effect of Oxidized Cholesterol on the Aorta of Rabbits- Scanning Electron Microscopic Observations

1982 ◽  
Vol 40 ◽  
pp. 340-341
Author(s):  
S. K. Pena ◽  
C. B. Taylor ◽  
J. Hill ◽  
J. Safarik
Keyword(s):  
Cholesterol Biosynthesis ◽  
Cholesterol Content ◽  
Arterial Injury ◽  
Electron Microscopic ◽  
Aortic Smooth Muscle ◽  
Oxidized Cholesterol ◽  
Initial Event ◽  
Membrane Structure And Function ◽  
Scanning Electron Microscopic ◽  
And Function

Introduction: Oxidized cholesterol derivatives have been demonstrated in various cell cultures to be very potent inhibitors of 3-hvdroxy-3- methylglutaryl Coenzyme A reductase which is a principle regulator of cholesterol biosynthesis in the cell. The cholesterol content in the cells exposed to oxidized cholesterol was found to be markedly decreased. In aortic smooth muscle cells, the potency of this effect was closely related to the cytotoxicity of each derivative. Furthermore, due to the similarity of their molecular structure to that of cholesterol, these oxidized cholesterol derivatives might insert themselves into the cell membrane, alter membrane structure and function and eventually cause cell death. Arterial injury has been shown to be the initial event of atherosclerosis.

Ultrastructure of developing visual cortical synapses in the cat superior colliculus

1991 ◽  
Vol 49 ◽  
pp. 156-157
Author(s):  
Caroline A. Miller ◽  
Laura L. Bruce
Keyword(s):  
Superior Colliculus ◽  
Phosphate Buffer ◽  
Receptive Fields ◽  
Visual Cortical Area ◽  
Cortical Synapses ◽  
Visual Cortical ◽  
And Function ◽  
Phosphate Buffered Saline ◽  
The Brain ◽  
Cat Superior Colliculus

The first visual cortical axons arrive in the cat superior colliculus by the time of birth. Adultlike receptive fields develop slowly over several weeks following birth. The developing cortical axons go through a sequence of changes before acquiring their adultlike morphology and function. To determine how these axons interact with neurons in the colliculus, cortico-collicular axons were labeled with biocytin (an anterograde neuronal tracer) and studied with electron microscopy.Deeply anesthetized animals received 200-500 nl injections of biocytin (Sigma; 5% in phosphate buffer) in the lateral suprasylvian visual cortical area. After a 24 hr survival time, the animals were deeply anesthetized and perfused with 0.9% phosphate buffered saline followed by fixation with a solution of 1.25% glutaraldehyde and 1.0% paraformaldehyde in 0.1M phosphate buffer. The brain was sectioned transversely on a vibratome at 50 μm. The tissue was processed immediately to visualize the biocytin.

Structural modifications of intercellular junctions.

1978 ◽  
Vol 36 (2) ◽  
pp. 330-331
Author(s):  
J. Metz ◽  
M. Merlo ◽  
W. G. Forssmann
Keyword(s):  
Gap Junctions ◽  
Intercellular Junctions ◽  
Cell Isolation ◽  
Extrahepatic Cholestasis ◽  
Structural Modifications ◽  
Pancreatic Duct Ligation ◽  
Pancreatic Cells ◽  
Duct Ligation ◽  
Thin Sectioning ◽  
And Function

Structure and function of intercellular junctions were studied under the electronmicroscope using conventional thin sectioning and freeze-etch replicas. Alterations of tight and gap junctions were analyzed 1. of exocrine pancreatic cells under cell isolation conditions and pancreatic duct ligation and 2. of hepatocytes during extrahepatic cholestasis.During the different steps of cell isolation of exocrine pancreatic cells, gradual changes of tight and gap junctions were observed. Tight junctions, which formed belt-like structures around the apex of control acinar cells in situ, subsequently diminished, became interrupted and were concentrated into macular areas (Fig. 1). Aggregations of membrane associated particles, which looked similar to gap junctions, were intermixed within tight junctional areas (Fig. 1). These structures continously disappeared in the last stages of the isolation procedure. The intercellular junctions were finally separated without destroying the integrity of the cell membrane, which was confirmed with porcion yellow, lanthanum chloride and horse radish peroxidase.

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