scholarly journals Origins of Protein Stability Revealed by Comparing Crystal Structures of TATA Binding Proteins

Structure ◽  
2004 ◽  
Vol 12 (1) ◽  
pp. 157-168 ◽  
Author(s):  
Hideaki Koike ◽  
Yoshie Kawashima-Ohya ◽  
Tomoko Yamasaki ◽  
Lester Clowney ◽  
Yoshio Katsuya ◽  
...  
Keyword(s):  
Protein Stability ◽  
Crystal Structures ◽  
Binding Proteins ◽  
Tata Binding Proteins

scholarly journals Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins

1997 ◽  
Vol 4 (3) ◽  
pp. 231-238 ◽  
Author(s):  
Charles Brenner ◽  
Preston Garrison ◽  
Jeffrey Gilmour ◽  
Daniel Peisach ◽  
Dagmar Ringe ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Proteins ◽  
Nucleotide Binding ◽  
Nucleotide Binding Proteins

scholarly journals Intersubunit linker length as a modifier of protein stability: Crystal structures and thermostability of mutant TRAP

2008 ◽  
Vol 17 (3) ◽  
pp. 518-526 ◽  
Author(s):  
Masahiro Watanabe ◽  
Yumiko Mishima ◽  
Ichiro Yamashita ◽  
Sam-Yong Park ◽  
Jeremy R.H. Tame ◽  
...  
Keyword(s):  
Protein Stability ◽  
Crystal Structures ◽  
Linker Length

Dimer Dissociation and Thermosensitivity Kinetics of theSaccharomycescerevisiaeand Human TATA Binding Proteins†

Biochemistry ◽  
1999 ◽  
Vol 38 (35) ◽  
pp. 11340-11348 ◽  
Author(s):  
Amy J. Jackson-Fisher ◽  
Sandeep Burma ◽  
Matthew Portnoy ◽  
Lumelle A. Schneeweis ◽  
Robert A. Coleman ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Tata Binding Proteins ◽  
Kinetics Of

scholarly journals Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis

IUCrJ ◽  
2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Sheng-Chia Chen ◽  
Li-Ci Ye ◽  
Te-Ming Yen ◽  
Ruei-Xin Zhu ◽  
Cheng-Yu Li ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
High Resolution ◽  
Protein Stability ◽  
Crystal Structures ◽  
Aspergillus Oryzae ◽  
Terminal Segment ◽  
Riboflavin Biosynthesis ◽  
The Third ◽  
Complex Forms ◽  
Deaminase Domain

Riboflavin serves as the direct precursor of the FAD/FMN coenzymes and is biosynthesized in most prokaryotes, fungi and plants. Fungal Rib2 possesses a deaminase domain for deamination of pyrimidine in the third step of riboflavin biosynthesis. Here, four high-resolution crystal structures of a Rib2 deaminase from Aspergillus oryzae (AoRib2) are reported which display three distinct occluded, open and complex forms that are involved in substrate binding and catalysis. In addition to the deaminase domain, AoRib2 contains a unique C-terminal segment which is rich in charged residues. Deletion of this unique segment has no effect on either enzyme activity or protein stability. Nevertheless, the C-terminal αF helix preceding the segment plays a role in maintaining protein stability and activity. Unexpectedly, AoRib2 is the first mononucleotide deaminase found to exist as a monomer, perhaps due to the assistance of its unique longer loops (Lβ1–β2, LαB–β3 and LαC–β4). These results form the basis for a molecular understanding of riboflavin biosynthesis in fungi and might assist in the development of antibiotics.

scholarly journals Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Garnish ◽  
Yanxiang Meng ◽  
Akiko Koide ◽  
Jarrod J. Sandow ◽  
Eric Denbaum ◽  
...  
Keyword(s):  
Cell Death ◽  
Plasma Membrane ◽  
Binding Site ◽  
Crystal Structures ◽  
Conformational Change ◽  
Binding Proteins ◽  
Conformational Transition ◽  
Human Cells ◽  
Conformational Interconversion ◽  
Large Conformational Change

AbstractPhosphorylation of the MLKL pseudokinase by the RIPK3 kinase leads to MLKL oligomerization, translocation to, and permeabilization of, the plasma membrane to induce necroptotic cell death. The precise choreography of MLKL activation remains incompletely understood. Here, we report Monobodies, synthetic binding proteins, that bind the pseudokinase domain of MLKL within human cells and their crystal structures in complex with the human MLKL pseudokinase domain. While Monobody-32 constitutively binds the MLKL hinge region, Monobody-27 binds MLKL via an epitope that overlaps the RIPK3 binding site and is only exposed after phosphorylated MLKL disengages from RIPK3 following necroptotic stimulation. The crystal structures identified two distinct conformations of the MLKL pseudokinase domain, supporting the idea that a conformational transition accompanies MLKL disengagement from RIPK3. These studies provide further evidence that MLKL undergoes a large conformational change upon activation, and identify MLKL disengagement from RIPK3 as a key regulatory step in the necroptosis pathway.

Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur

2015 ◽  
Vol 68 (3) ◽  
pp. 385 ◽  
Author(s):  
Hanzala B. Hussain ◽  
Katie A. Wilson ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Protein Stability ◽  
Crystal Structures ◽  
Protein Complexes ◽  
Aromatic Amino Acids ◽  
Biological Macromolecules ◽  
Great Stability ◽  
Π Interactions ◽  
And Function

Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.

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