Side chain-directed assembly of triangular molecular panels into a tetrahedron vs. open coneElectronic supplementary information (ESI) available: physical properties of open cone 4 with mesitylene and CBr4. See http://www.rsc.org/suppdata/cc/b3/b305129c/

2003 ◽  
pp. 1808 ◽  
Author(s):  
Michito Yoshizawa ◽  
Muneki Nagao ◽  
Kazuhiko Umemoto ◽  
Kumar Biradha ◽  
Makoto Fujita ◽  
...  
Keyword(s):  
Physical Properties ◽  
Directed Assembly ◽  
Supplementary Information ◽  
Side Chain ◽  
Open Cone

A study of the relationships of interactions between Asp-201, Na+ or K+, and galactosyl C6 hydroxyl and their effects on binding and reactivity of β-galactosidase

2004 ◽  
Vol 82 (2) ◽  
pp. 275-284 ◽  
Author(s):  
Julia Xu ◽  
Mary A.A McRae ◽  
Scott Harron ◽  
Beatrice Rob ◽  
Reuben E Huber
Keyword(s):  
Physical Properties ◽  
Negative Charge ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Sodium Potassium ◽  
The Difference ◽  
Potassium Binding ◽  
Covalent Intermediate ◽  
Catalytic Effects

The interactions between Na+ (and K+) and Asp-201 of β-galactosidase were studied. Analysis of the changes in Km and Vmax showed that the Kd for Na+ of wild type β-galactosidase (0.36 ± 0.09 mM) was about 10× lower than for K+ (3.9 ± 0.6 mM). The difference is probably because of the size and other physical properties of the ions and the binding pocket. Decreases of Km as functions of Na+ and K+ for oNPG and pNPG and decreases of the Ki of both shallow and deep mode inhibitors were similar, whereas the Km and Ki of substrates and inhibitors without C6 hydroxyls remained constant. Thus, Na+ and K+ are important for binding galactosyl moieties via the C6 hydroxyl throughout catalysis. Na+ and K+ had lesser effects on the Vmax. The Vmax of pNPF and pNPA (substrates that lack a C6 hydroxyl) did not change upon addition of Na+ or K+, showing that the catalytic effects are also mediated via the C6 hydroxyl. Arrhenius plots indicated that Na+, but not K+, caused k3 (degalactosylation) to increase. Na+ also caused the k2 (galactosylation) with oNPG, but not with pNPG, to increase. In contrast, K+ caused the k2 values with both oNPG and pNPG to increase. Na+ and K+ mainly altered the entropies of activation of k2 and k3 with only small effects on the enthalpies of activation. This strongly suggests that only the positioning of the substrate, transition states, and covalent intermediate are altered by Na+ and K+. Further evidence that positioning is important was that substitution of Asp-201 with a Glu caused the Km and Ki values to increase significantly. In addition, the Kd values for Na+ or K+ were 5 to 8 fold higher. The negative charge of Asp-201 was shown to be vital for Na+ and K+ binding. Large amounts of Na+ or K+ had no effect on the very large Km and Ki values of D201N-β-galactosidase and the Vmax values changed minimally and in a linear rather than hyperbolic way. D201F-β-galactosidase, with a very bulky hydrophobic side chain in place of Asp, essentially obliterated all binding and catalysis.Key words: β-galactosidase, sodium, potassium, binding, aspartic acid.

ChemInform Abstract: Synthesis of 2,2′-Bipyridines Bearing Amino or Carboxyl Group at the Side Chain and Physical Properties of Their Ruthenium(II) Complexes.

ChemInform ◽  
2010 ◽  
Vol 30 (24) ◽  
pp. no-no
Author(s):  
Akira Katoh ◽  
Yoshihiro Kitamura ◽  
Hideyuki Fujii ◽  
Yumi Horie ◽  
Tetsuji Satoh ◽  
...  
Keyword(s):  
Physical Properties ◽  
Side Chain ◽  
Carboxyl Group

scholarly journals Heterometal Grafted metalla-ynes and Poly(metalla-ynes): A Review on Structure–Property Relationships and Applications

Polymers ◽  
2021 ◽  
Vol 13 (21) ◽  
pp. 3654
Author(s):  
Rayya A. Al-Balushi ◽  
Ashanul Haque ◽  
Idris J. Al-Busaidi ◽  
Houda Al-Sharji ◽  
Muhammad S. Khan
Keyword(s):  
Physical Properties ◽  
Main Chain ◽  
Functional Materials ◽  
Photo Luminescence ◽  
Structural Features ◽  
Side Chain ◽  
Structure Property ◽  
Molecular Scaffolds ◽  
Structure Property Relationships ◽  
Rigid Rod

Metalla-ynes and poly(metalla-ynes) have emerged as unique molecular scaffolds with fascinating structural features and intriguing photo-luminescence (PL) properties. Their rigid-rod conducting backbone with tunable photo-physical properties has generated immense research interests for the design and development of application-oriented functional materials. Introducing a second d- or f-block metal fragment in the main-chain or side-chain of a metalla-yne and poly(metalla-yne) was found to further modulate the underlying features/properties. This review focuses on the photo-physical properties and opto-electronic (O-E) applications of heterometal grafted metalla-ynes and poly(metalla-ynes).

scholarly journals Side Chain-Directed Assembly of Large Discotic π-Conjugated Molecules: Toward Tuning and Stabilization of Mesophases

2015 ◽  
Vol 28 (4) ◽  
pp. 583-587 ◽  
Author(s):  
Yusuke Tsutsui ◽  
Tsuneaki Sakurai ◽  
Kenichi Kato ◽  
Masaki Takata ◽  
Shu Seki
Keyword(s):  
Directed Assembly ◽  
Side Chain ◽  
Conjugated Molecules

scholarly journals Linear poly(alkyl ethylene imine) with varying side chain length: synthesis and physical properties

2010 ◽  
Vol 1 (5) ◽  
pp. 747 ◽  
Author(s):  
Hanneke M. L. Lambermont-Thijs ◽  
Lies Bonami ◽  
Filip E. Du Prez ◽  
Richard Hoogenboom
Keyword(s):  
Physical Properties ◽  
Chain Length ◽  
Side Chain ◽  
Ethylene Imine ◽  
Side Chain Length ◽  
Linear Poly

scholarly journals FASPR: an open-source tool for fast and accurate protein side-chain packing

2020 ◽  
Vol 36 (12) ◽  
pp. 3758-3765 ◽  
Author(s):  
Xiaoqiang Huang ◽  
Robin Pearce ◽  
Yang Zhang
Keyword(s):  
Protein Structure ◽  
Protein Design ◽  
Structure Prediction ◽  
Protein Structures ◽  
Scoring Function ◽  
Supplementary Information ◽  
Side Chain ◽  
Chain Packing ◽  
And Function ◽  
Side Chain Packing

Abstract Motivation Protein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory. Results We present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20°, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3 s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies. Availability and implementation The web server, source code and datasets are freely available at https://zhanglab.ccmb.med.umich.edu/FASPR and https://github.com/tommyhuangthu/FASPR. Supplementary information Supplementary data are available at Bioinformatics online.

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