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

scholarly journals Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sara Linse ◽  
Eva Thulin ◽  
Hanna Nilsson ◽  
Johannes Stigler
Keyword(s):  
Ligand Binding ◽  
Protein Stability ◽  
Extreme Case ◽  
Bound State ◽  
Marginal Effect ◽  
Length Variation ◽  
Loop Length ◽  
Linker Length ◽  
Single Domain Protein ◽  
Calbindin D

AbstractProtein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.

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.

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.

Structure Analysis of Two CheY Mutants: Importance of the Hydrogen-Bond Contribution to Protein Stability

1998 ◽  
Vol 54 (3) ◽  
pp. 378-385 ◽  
Author(s):  
Deborah Wilcock ◽  
María Teresa Pisabarro ◽  
Eva López-Hernandez ◽  
Luis Serrano ◽  
Miquel Coll
Keyword(s):  
Hydrogen Bond ◽  
Protein Stability ◽  
Crystal Structures ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Polar Group ◽  
Hydrophobic Core ◽  
Hydrogen Bonding Pattern ◽  
The Stability ◽  
Α Helix

The crystal structures of two double mutants (F14N/V21T and F14N/V86T) of the signal transduction protein CheY have been determined to a resolution of 2.4 and 2.2 Å, respectively. The structures were solved by molecular replacement and refined to final R values of 18.4 and 19.2%, respectively. Together with urea-denaturation experiments the structures have been used to analyse the effects of mutations where hydrophobic residues are replaced by residues capable of establishing hydrogen bonds. The large increase in stabilization (−12.1 kJ mol−1) of the mutation Phe14Asn arises from two factors: a reverse hydrophobic effect and the formation of a good N-cap at α-helix 1. In addition, a forward–backward hydrogen-bonding pattern, resembling an N-capping box and involving Asn14 and Arg18, has been found. The two Val to Thr mutations at the hydrophobic core have different thermodynamic effects: the mutation Val21Thr does not affect the stability of the protein while the mutation Val86Thr causes a small destabilization of 1.7 kJ mol−1. At site 21 a backward side-chain-to-backbone hydrogen bond is formed inside α-helix 1 with the carbonyl O atom of the i − 4 residue without movement of the mutated side chain. The destabilizing effect of introducing a polar group in the core is efficiently compensated for by the formation of an extra hydrogen bond. At site 86 the new Oγ atom escapes from the hydrophobic environment by a χ1 rotation into an adjacent hydrophilic cavity to form a new hydrogen bond. In this case the isosteric Val to Thr substitution is disruptive but the loss in stabilization energy is partly compensated by the formation of a hydrogen bond. The two crystal structures described in this work underline the significance of the hydrogen-bond component to protein stability.

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

Pollutant Identification by Selected Area Electron Diffraction

1974 ◽  
Vol 32 ◽  
pp. 532-533
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson ◽  
C. W. Walker
Keyword(s):  
Thermal Treatment ◽  
Electron Diffraction ◽  
Sample Preparation ◽  
Crystal Structures ◽  
Water Samples ◽  
Environmental Samples ◽  
Short Review ◽  
Selected Area Electron Diffraction ◽  
Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

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