X-ray crystallographic validation of structure predictions used in computational design for protein stabilization

2015 ◽  
Vol 83 (5) ◽  
pp. 940-951 ◽  
Author(s):  
Robert J. Floor ◽  
Hein J. Wijma ◽  
Peter A. Jekel ◽  
Anke C. Terwisscha van Scheltinga ◽  
Bauke W. Dijkstra ◽  
...  
Science ◽  
2020 ◽  
Vol 369 (6508) ◽  
pp. 1227-1233 ◽  
Author(s):  
Nicholas F. Polizzi ◽  
William F. DeGrado

The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure—a van der Mer (vdM)—that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug–protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.


2019 ◽  
Vol 11 (19) ◽  
pp. 2491-2504 ◽  
Author(s):  
Matthias R Bauer ◽  
Rhiannon N Jones ◽  
Raysa K Tareque ◽  
Bradley Springett ◽  
Felix A Dingler ◽  
...  

Aim: The p53 cancer mutation Y220C creates a conformationally unstable protein with a unique elongated surface crevice that can be targeted by molecular chaperones. We report the structure-guided optimization of the carbazole-based stabilizer PK083. Materials & methods: Biophysical, cellular and x-ray crystallographic techniques have been employed to elucidate the mode of action of the carbazole scaffolds. Results: Targeting an unoccupied subsite of the surface crevice with heterocycle-substituted PK083 analogs resulted in a 70-fold affinity increase to single-digit micromolar levels, increased thermal stability and decreased rate of aggregation of the mutant protein. PK9318, one of the most potent binders, restored p53 signaling in the liver cancer cell line HUH-7 with homozygous Y220C mutation. Conclusion: The p53-Y220C mutant is an excellent paradigm for the development of mutant p53 rescue drugs via protein stabilization. Similar rescue strategies may be applicable to other cavity-creating p53 cancer mutations.


2017 ◽  
Vol 114 (47) ◽  
pp. 12472-12477 ◽  
Author(s):  
Eric J. Moore ◽  
Dmitri Zorine ◽  
William A. Hansen ◽  
Sagar D. Khare ◽  
Rudi Fasan

Thermostabilization represents a critical and often obligatory step toward enhancing the robustness of enzymes for organic synthesis and other applications. While directed evolution methods have provided valuable tools for this purpose, these protocols are laborious and time-consuming and typically require the accumulation of several mutations, potentially at the expense of catalytic function. Here, we report a minimally invasive strategy for enzyme stabilization that relies on the installation of genetically encoded, nonreducible covalent staples in a target protein scaffold using computational design. This methodology enables the rapid development of myoglobin-based cyclopropanation biocatalysts featuring dramatically enhanced thermostability (ΔTm = +18.0 °C and ΔT50 = +16.0 °C) as well as increased stability against chemical denaturation [ΔCm (GndHCl) = 0.53 M], without altering their catalytic efficiency and stereoselectivity properties. In addition, the stabilized variants offer superior performance and selectivity compared with the parent enzyme in the presence of a high concentration of organic cosolvents, enabling the more efficient cyclopropanation of a water-insoluble substrate. This work introduces and validates an approach for protein stabilization which should be applicable to a variety of other proteins and enzymes.


2005 ◽  
Vol 351 (5) ◽  
pp. 1160-1168 ◽  
Author(s):  
Michael Wunderlich ◽  
Andreas Martin ◽  
Claudia A. Staab ◽  
Franz X. Schmid

Author(s):  
Immanuel Reim ◽  
Giovanni Occhipinti ◽  
Karl W. Törnroos ◽  
Deryn E. Fogg ◽  
Vidar R. Jensen

AbstractThe selective transformation of 1-alkenes into E-olefins is a long-standing challenge in olefin metathesis. Density functional theory (DFT) calculations predict high E-selectivity for catalysts incorporating a bidentate, dianionic thio-indolate ligand within a RuXX’(NHC)(py)(= CHR) platform (NHC = N-heterocyclic carbene; py = pyridine). Such complexes are predicted to yield E-olefins by favoring anti-disposed substituents in the transition state expected to be rate-determining: specifically, that for cycloreversion of the metallacyclobutane intermediate. Three pyridine-stabilized catalysts Ru21a-c were synthesized, in which the thio-indolate ligand bears a H, Me, or Ph substituent at the C2 position, and the NHC ligand is the unsaturated imidazoline-2-ylidene Me2IMes (which bears N-mesityl groups and methyl groups on the C4,5 backbone). Single-crystal X-ray diffraction analysis of Ru21c confirms the ligand orientation required for E-selective metathesis, with the thio-indolate sulfur atom binding cis to the NHC, and the indolate nitrogen atom trans to the NHC. However, whereas the new complexes mediated metathetic exchange of their 2-thienylmethylidene ligand in the presence of the common metathesis substrates styrene and allylbenzene, no corresponding self-metathesis products were obtained. Only small amounts of 2-butene (73% (Z)-2-butene) were obtained in self-metathesis of propene using Ru21a. Detailed DFT analysis of this process revealed that product release is surprisingly slow, limiting the reaction rate and explaining the low metathesis activity. With the barrier to dissociation of (Z)-2-butene being lower than that of (E)-2-butene, the calculations also account for the observed Z-selectivity of Ru21a. These findings provide guidelines for catalyst redesign in pursuit of the ambitious goal of E-selective 1-alkene metathesis. Graphic abstract


2016 ◽  
Vol 72 (a1) ◽  
pp. s257-s257
Author(s):  
Marco Dal Lago ◽  
Hein J. Wijma ◽  
Anke C. Terwisscha van Scheltinga ◽  
Dick B. Janssen ◽  
Andy-Mark W. H. Thunnissen

Science ◽  
2021 ◽  
Vol 371 (6531) ◽  
pp. eabc8182
Author(s):  
Anastassia A. Vorobieva ◽  
Paul White ◽  
Binyong Liang ◽  
Jim E. Horne ◽  
Asim K. Bera ◽  
...  

Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a “hypothesis, design, and test” approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.


1994 ◽  
Vol 144 ◽  
pp. 275-277
Author(s):  
M. Karlický ◽  
J. C. Hénoux

AbstractUsing a new ID hybrid model of the electron bombardment in flare loops, we study not only the evolution of densities, plasma velocities and temperatures in the loop, but also the temporal and spatial evolution of hard X-ray emission. In the present paper a continuous bombardment by electrons isotropically accelerated at the top of flare loop with a power-law injection distribution function is considered. The computations include the effects of the return-current that reduces significantly the depth of the chromospheric layer which is evaporated. The present modelling is made with superthermal electron parameters corresponding to the classical resistivity regime for an input energy flux of superthermal electrons of 109erg cm−2s−1. It was found that due to the electron bombardment the two chromospheric evaporation waves are generated at both feet of the loop and they propagate up to the top, where they collide and cause temporary density and hard X-ray enhancements.


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