LitCovid-sentences  

PMC:7605337 / 49730-51701 JSONTXT 6 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T337 0-206 Sentence denotes The total binding energy calculation of all the variants showed that mutation Y489A has the highest binding affinity among all systems which is about 11 kcal/mol stronger than that of the nCOV-2019 complex.
T338 207-305 Sentence denotes This residue is located in β6, which is part of the recognition region of RBD for binding to ACE2.
T339 306-480 Sentence denotes Removal of this bulky hydrophobic residue at the interface with ACE2 caused the extended loop to move closer to the ACE2 interface and make more H-bonds with ACE2 (Table S3).
T340 481-608 Sentence denotes A high electrostatic interaction energy is the reason for the higher binding energy of mutant Y489A than the wild-type complex.
T341 609-800 Sentence denotes It is interesting to note that among the five residues L455, F456, Y473, A475, and Y489 that make hydrophobic interactions with ACE2, Y489 is the only residue that is conserved from SARS-COV.
T342 801-962 Sentence denotes However, the experimental binding affinity measurements using deep mutational scanning showed that mutations at this position lower the binding affinity to ACE2.
T343 963-1044 Sentence denotes Other alanine substitutions that increase the binding energy are G446A and G447A.
T344 1045-1179 Sentence denotes Residues G446 and G447 reside in L1 and mutation to alanine can make L1 take a more rigid form as shown in the RMSF plot in Figure S3.
T345 1180-1513 Sentence denotes However, experiment showed that these mutations have similar or lower binding affinities to ACE2 than the wild-type RBD and care must be taken when interpreting these results.25 This discrepancy could be due to force-field inaccuracy and the deficiencies in the PBSA method for the treatment of solvent in binding energy calculation.
T346 1514-1623 Sentence denotes Further studies are needed to investigate whether these mutations will increase the binding affinity to ACE2.
T347 1624-1971 Sentence denotes Deep mutational scanning using flow cytometry is a qualitative method to measure the impact of a large number of mutations of protein–protein interactions and further experiments such as SPR or isothermal titration calorimetry which are conventional methods for measuring binding affinities needed to study the effect of these mutations in detail.