scholarly journals New Strategy for Reversible Modulation of Protein Activity through Site-Specific Conjugation of Small Molecule and Polymer

2014 ◽  
Vol 25 (7) ◽  
pp. 1252-1260 ◽  
Author(s):  
Lei Wang ◽  
Lin Yuan ◽  
Hongwei Wang ◽  
Xiaoli Liu ◽  
Xinming Li ◽  
...  
2019 ◽  
Vol 15 ◽  
pp. P265-P265
Author(s):  
Wenhai Huang ◽  
Wenting Du ◽  
Xiaoliang Zheng ◽  
Beibei Wang ◽  
Zhengrong Shen

2019 ◽  
Vol 5 (3) ◽  
pp. eaav8423 ◽  
Author(s):  
Yanxiang Cui ◽  
Kang Zhou ◽  
David Strugatsky ◽  
Yi Wen ◽  
George Sachs ◽  
...  

The urea channel ofHelicobacterpylori(HpUreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication ofH. pylori. Here, we present the cryo-EM structures ofHpUreI in closed and open conformations, both at a resolution of 2.7 Å. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy forH. pylorieradication.


2018 ◽  
Vol 114 (3) ◽  
pp. 58a
Author(s):  
Thomas E. Frederick ◽  
Kathryn M. Hart ◽  
Katelyn E. Moeder ◽  
Chris M.W. Ho ◽  
Maxwell I. Zimmerman ◽  
...  

Biochemistry ◽  
2003 ◽  
Vol 42 (22) ◽  
pp. 6735-6746 ◽  
Author(s):  
Zhiwen Zhang ◽  
Brian A. C. Smith ◽  
Lei Wang ◽  
Ansgar Brock ◽  
Charles Cho ◽  
...  

2019 ◽  
Author(s):  
Kevin Dalton ◽  
Tom Lopez ◽  
Vijay Pande ◽  
Judith Frydman

AbstractSite-specific labeling of proteins is often a prerequisite for biophysical and biochemical characterization. Chemical modification of a unique cysteine residue is among the most facile methods for site-specific labeling of proteins. However, many proteins have multiple reactive cysteines, which must be mutated to other residues to enable labeling of unique positions. This trial-and-error process often results in cysteine-free proteins with reduced activity or stability. Herein we describe a general methodology to rationally engineer cysteine-less proteins. Briefly, natural variation across orthologues is exploited to identify suitable cysteine replacements compatible with protein activity and stability. As a proof-of-concept, we recount the successful engineering of a cysteine-less mutant of the group II chaperonin from methanogenic archaeon Methanococcus maripaludis. A webapp, REP-X (Replacement at Endogenous Positions from eXtant sequences), which enables users to design their own cysteine-less protein variants, will make this rational approach widely available.


2019 ◽  
Author(s):  
Stephanie Cara Bishop ◽  
Robert Winefield ◽  
Asokan Anbanandam ◽  
Jed Noah Lampe

The lanthanides (Ln3+), or rare earth elements, have proven to be useful tools for biomolecular NMR, X-ray crystallographic, and fluorescence analyses due to their unique 4f orbitals. However, their utility in biological applications has been limited because site-specific incorporation of a chelating element is required to ensure efficient binding of the free Ln3+ ion. Additionally, current Ln3+ chelator syntheses complicate efforts to directly incorporate Ln3+ chelators into proteins as the multi-step processes and a reliance on organic solvents promote protein denaturation and aggregation which are generally incompatible with direct incorporation into the protein of interest. To overcome these limitations, herein we describe a two-step aqueous synthesis of a small molecule lanthanide chelating agent amenable to site-specific incorporation into a protein using copper-free click chemistry with unnatural amino acids. The bioconjugate combines a diethylenetriaminepentaacetic acid (DTPA) chelating moiety with a clickable dibenzylcyclooctyne-amine (DBCO-amine) to facilitate the reaction with an azide containing unnatural amino acid. Incorporating the DBCO-amine avoids the use of the cytotoxic Cu2+ ion as a catalyst. The clickable lanthanide chelator (CLC) reagent reacted readily with p-azidophenylalanine (paF) without the need of a copper catalyst, thereby demonstrating proof-of-concept. Implementation of the orthogonal click chemistry reaction has the added advantage that the chelator can be used directly in a protein labeling reaction, without the need of extensive purification. Given the inherent advantages of Cu2+-free click chemistry, aqueous synthesis, and facile labeling, we believe that the CLC will find abundant use in both structural and biophysical studies of proteins and their complexes.


2015 ◽  
Vol 1 (9) ◽  
pp. e1500633 ◽  
Author(s):  
Yan Guan ◽  
Xiaonan Shan ◽  
Fenni Zhang ◽  
Shaopeng Wang ◽  
Hong-Yuan Chen ◽  
...  

Measuring small molecule interactions with membrane proteins in single cells is critical for understanding many cellular processes and for screening drugs. However, developing such a capability has been a difficult challenge. We show that molecular interactions with membrane proteins induce a mechanical deformation in the cellular membrane, and real-time monitoring of the deformation with subnanometer resolution allows quantitative analysis of small molecule–membrane protein interaction kinetics in single cells. This new strategy provides mechanical amplification of small binding signals, making it possible to detect small molecule interactions with membrane proteins. This capability, together with spatial resolution, also allows the study of the heterogeneous nature of cells by analyzing the interaction kinetics variability between different cells and between different regions of a single cell.


2015 ◽  
Vol 51 (80) ◽  
pp. 14885-14888 ◽  
Author(s):  
Norihiro Sato ◽  
Genichiro Tsuji ◽  
Yoshihiro Sasaki ◽  
Akira Usami ◽  
Takuma Moki ◽  
...  

In this communication, we report a new strategy for the selective alkylation of DNA using an oligonucleotide containing an abasic site and alkylating probes.


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