scholarly journals Covalent Flexible Peptide Docking in Rosetta

2021 ◽  
Author(s):  
Barr Tivon ◽  
Ronen Gabizon ◽  
Bente A Somsen ◽  
Peter J Cossar ◽  
Christian Ottmann ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Peptide Docking

Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains...

Aldehyde gold clusters for molecular labeling

1995 ◽  
Vol 53 ◽  
pp. 858-859
Author(s):  
James F. Hainfeld ◽  
Frederic R. Furuya
Keyword(s):  
Covalent Bond ◽  
Aldehyde Group ◽  
Gold Clusters ◽  
Side Reactions ◽  
Amino Groups ◽  
Sodium Cyanoborohydride ◽  
Schiff’S Base ◽  
Protein Molecules ◽  
Hydroxysuccinimide Esters ◽  
Primary Amino

Glutaraldehyde is a useful tissue and molecular fixing reagents. The aldehyde moiety reacts mainly with primary amino groups to form a Schiff's base, which is reversible but reasonably stable at pH 7; a stable covalent bond may be formed by reduction with, e.g., sodium cyanoborohydride (Fig. 1). The bifunctional glutaraldehyde, (CHO-(CH2)3-CHO), successfully stabilizes protein molecules due to generally plentiful amines on their surface; bovine serum albumin has 60; 59 lysines + 1 α-amino. With some enzymes, catalytic activity after fixing is preserved; with respect to antigens, glutaraldehyde treatment can compromise their recognition by antibodies in some cases. Complicating the chemistry somewhat are the reported side reactions, where glutaraldehyde reacts with other amino acid side chains, cysteine, histidine, and tyrosine. It has also been reported that glutaraldehyde can polymerize in aqueous solution. Newer crosslinkers have been found that are more specific for the amino group, such as the N-hydroxysuccinimide esters, and are commonly preferred for forming conjugates. However, most of these linkers hydrolyze in solution, so that the activity is lost over several hours, whereas the aldehyde group is stable in solution, and may have an advantage of overall efficiency.

Structure of stacking faults in pyrite using TEM techniques

1992 ◽  
Vol 50 (1) ◽  
pp. 358-359
Author(s):  
Raja Subramanian ◽  
Kenneth S. Vecchio
Keyword(s):  
Lattice Structure ◽  
Stacking Faults ◽  
Covalent Bond ◽  
Group Symmetry ◽  
Iron Pyrite ◽  
Dislocation Glide ◽  
Partial Dislocations ◽  
Transmission Electron ◽  
Contrast Analysis ◽  
Chlorine Ions

The structure of stacking faults and partial dislocations in iron pyrite (FeS2) have been studied using transmission electron microscopy. Pyrite has the NaCl structure in which the sodium ions are replaced by iron and chlorine ions by covalently-bonded pairs of sulfur ions. These sulfur pairs are oriented along the <111> direction. This covalent bond between sulfur atoms is the strongest bond in pyrite with Pa3 space group symmetry. These sulfur pairs are believed to move as a whole during dislocation glide. The lattice structure across these stacking faults is of interest as the presence of these stacking faults has been preliminarily linked to a higher sulfur reactivity in pyrite. Conventional TEM contrast analysis and high resolution lattice imaging of the faulted area in the TEM specimen has been carried out.

Effect of Integral Proteins on Frozen Membrane Fracture

1980 ◽  
Vol 38 ◽  
pp. 756-759 ◽  
Author(s):  
S. Kirchanski ◽  
D. Branton
Keyword(s):  
Lipid Bilayers ◽  
Freeze Fracture ◽  
Covalent Bond ◽  
Erythrocyte Membranes ◽  
Glycophorin A ◽  
Experimental Protocol ◽  
Transmembrane Glycoprotein ◽  
Bond Breakage ◽  
Human Erythrocyte Membranes ◽  
Integral Proteins

We have investigated the effect of integral membrane proteins upon the fracturing of frozen lipid bilayers. This investigation has been part of an effort to develop freeze fracture labeling techniques and to assess the possible breakage of covalent protein bonds during the freeze fracture process. We have developed an experimental protocol utilizing lectin affinity columns which should detect small amounts of covalent bond breakage during the fracture of liposomes containing purified (1) glycophorin (a transmembrane glycoprotein of human erythrocyte membranes). To fracture liposomes in bulk, frozen liposomes are ground repeatedly under liquid nitrogen. Failure to detect any significant covalent bond breakage (contrary to (2)) led us to question the effectiveness of our grinding procedure in fracturing and splitting lipid bilayers.

Chemically Fueled Assembly of Macrocycles Comprising Multiple Transient Bonds

2019 ◽  
Author(s):  
Mohammad Mosharraf Hossain ◽  
Joshua Atkinson ◽  
Scott Hartley
Keyword(s):  
Covalent Bond ◽  
Dicarboxylic Acids ◽  
Molecular Assembly ◽  
Chemical Systems ◽  
Complex Architectures ◽  
The Creation ◽  
Dynamic Exchange

Dissipative (nonequilibrium) assembly powered by chemical fuels has great potential for the creation of new adaptive chemical systems. However, while molecular assembly at equilibrium is routinely used to prepare complex architectures from polyfunctional monomers, species formed out of equilibrium have, to this point, been structurally very simple. In most examples the fuel simply effects the formation of a single transient covalent bond. Here, we show that chemical fuels can assemble bifunctional components into macrocycles containing multiple transient bonds. Specifically, dicarboxylic acids give aqueous dianhydride macrocycles on treatment with a carbodiimide. The macrocycle is assembled efficiently as a consequence of both fuel-dependent and -independent mechanisms: it undergoes slower decomposition, building up as the fuel recycles the components, and is a favored product of the dynamic exchange of the anhydride bonds. These results create new possibilities for generating structurally sophisticated out-of-equilibrium species.

Chemically Fueled Assembly of Macrocycles Comprising Multiple Transient Bonds

2019 ◽  
Author(s):  
Mohammad Mosharraf Hossain ◽  
Joshua Atkinson ◽  
Scott Hartley
Keyword(s):  
Covalent Bond ◽  
Dicarboxylic Acids ◽  
Molecular Assembly ◽  
Chemical Systems ◽  
Complex Architectures ◽  
The Creation ◽  
Dynamic Exchange

Dissipative (nonequilibrium) assembly powered by chemical fuels has great potential for the creation of new adaptive chemical systems. However, while molecular assembly at equilibrium is routinely used to prepare complex architectures from polyfunctional monomers, species formed out of equilibrium have, to this point, been structurally very simple. In most examples the fuel simply effects the formation of a single transient covalent bond. Here, we show that chemical fuels can assemble bifunctional components into macrocycles containing multiple transient bonds. Specifically, dicarboxylic acids give aqueous dianhydride macrocycles on treatment with a carbodiimide. The macrocycle is assembled efficiently as a consequence of both fuel-dependent and -independent mechanisms: it undergoes slower decomposition, building up as the fuel recycles the components, and is a favored product of the dynamic exchange of the anhydride bonds. These results create new possibilities for generating structurally sophisticated out-of-equilibrium species.

EFEKTIVITAS MODEL PEMBELAJARAN KOOPERATIF TIPE TEAMS GAMES TOURNAMENT (TGT) BERBANTUAN MEDIA KARTU SOAL PADA SUB MATERI IKATAN KOVALEN KELAS X MIA DI SMA ISLAM HARUNIYAH PONTIANAK

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Zulfadhli Abdillah
Keyword(s):  
Student Learning ◽  
Learning Outcomes ◽  
Covalent Bond ◽  
Student Learning Outcomes ◽  
Learning Model ◽  
Covalent Bonds ◽  
Team Games ◽  
Bonding Material ◽  
Before And After ◽  
Tenth Grade

 This  study  is  motivated  by  the  low  learning  outcomes  in  the  Sub-covalent  Bond class of tenth-grade students, SMA Islam Haruniyah Pontianak. This problem is due to the  lack  of  students'  understanding  of  the  concept  of  Covalent  Bonds.  Therefore,  a proper learning model is required to improve students’ understanding of Covalent Bond concepts  based  on  the  characteristics  of  both  learning  materials    and  students.  This study  aimed  to  investigate  the  differences  in  the  student  learning  outcomes  and  the effectiveness of the question card-based on TGT learning in the Sub-covalent Bonding material. Using the pre-experimental method of one-group pretest-posttest design, the tenth-grade  students  of  Math  and  Science  Class  of  SMS  Islam  Haruniyah  Pontianak participated in this study. The data collection tools used were learning outcomes tests, observation sheets, and interview sheets. The results of data analysis revealed that the average  pretest  score  was  36  and  the  posttest  was  62.94.  In  addition,  the  t-test statistical  analysis  indicated  a  significance  value  of  0.00  (0.00  <0.05)  which  meanth that there were differences in student learning outcomes between before and after the question  card-based  TGT  learning  model  implemented.  The  gain  value  was  0.42.  In other words, the  question card-based on TGT learning model is effective in improving the student  learning outcomes with good category. Keywords: Covalent Bond, Question Card, Team Games Tournament (TGT)

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