FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1981907708> ?p ?o ?g. }

• W1981907708 endingPage "245" @default.
• W1981907708 startingPage "226" @default.
• W1981907708 abstract "We present calculations of the absolute and relative binding free energies of complexation of streptavidin with biotin and its analogs by means of a thermodynamic free energy perturbation method implemented with molecular dynamics. Using the recently solved crystal structure of the streptavidin-biotin complex, biotin was mutated into a dummy molecule as well as thiobiotin and iminobiotin both in the protein and in solution. The calculated absolute binding free energy was dependent on the simulation model used. Encouragingly, the best models provided a reasonable semiquantitative reproduction (-20 to -22 kcal/mol) of the experimental free energy (-18.3 kcal/mol). Furthermore, the calculated results give clear insights into the binding nature of the protein-ligand complex, showing that the van der Waals energy dominates the electrostatic and hydrogen bonding energies in the binding of biotin by streptavidin. Specifically, the mutation of biotin into a dummy molecule in solution has a delta G (van der Waals) approximately -4 kcal/mol, due to the cancellation of dispersion and repulsion cavity effects. On the other hand, in the protein, a very small free energy price must be paid to create a cavity since one already exists and the mutation of biotin into a dummy molecule has a delta G (van der Waals) approximately 15 kcal/mol. These results are also consistent with the interpretation that the entropy increase to be expected from hydrophobic interactions from desolvation of biotin is counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds, which have been derived from the apparently conflicting experimental data. They provide an alternative interpretation of the reason for the extremely high affinity of the biotin-streptavidin interaction than that recently proposed by Weber et al. (J. Am. Chem. Soc. 114:3197, 1992). In the case of the relative binding free energies, the calculated values of 3.8 +/- 0.6 and 7.2 +/- 0.6 kcal/mol compare well with the experimental values of 3.6 and 6.2 kcal/mol for the perturbation of biotin to thiobiotin and iminobiotin, respectively in the related protein avidin. The calculations indicate that desolvation of the ligand is important in understanding the relative affinity of the ligands with the protein. The above successful simulations suggest that the molecular dynamics/free energy perturbation method is useful for understanding the energetic features affecting the binding between proteins and ligands, since it is generally difficult to determine these factors unambiguously by experiment.(ABSTRACT TRUNCATED AT 400 WORDS)" @default.
• W1981907708 created "2016-06-24" @default.
• W1981907708 creator A5033385040 @default.
• W1981907708 creator A5086615420 @default.
• W1981907708 date "1993-07-01" @default.
• W1981907708 modified "2023-10-16" @default.
• W1981907708 title "Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches" @default.
• W1981907708 cites W1511967000 @default.
• W1981907708 cites W1533012833 @default.
• W1981907708 cites W157808733 @default.
• W1981907708 cites W1754901624 @default.
• W1981907708 cites W1892938473 @default.
• W1981907708 cites W1963523261 @default.
• W1981907708 cites W1976499671 @default.
• W1981907708 cites W1976870460 @default.
• W1981907708 cites W1977104435 @default.
• W1981907708 cites W1977902160 @default.
• W1981907708 cites W1978823851 @default.
• W1981907708 cites W1979046104 @default.
• W1981907708 cites W1983348238 @default.
• W1981907708 cites W1983910978 @default.
• W1981907708 cites W1989651518 @default.
• W1981907708 cites W1991040759 @default.
• W1981907708 cites W1992118967 @default.
• W1981907708 cites W1994826811 @default.
• W1981907708 cites W2007434121 @default.
• W1981907708 cites W2019962781 @default.
• W1981907708 cites W2021284440 @default.
• W1981907708 cites W2027261646 @default.
• W1981907708 cites W2027836552 @default.
• W1981907708 cites W2031972197 @default.
• W1981907708 cites W2035266068 @default.
• W1981907708 cites W2036623463 @default.
• W1981907708 cites W2047256112 @default.
• W1981907708 cites W2048740371 @default.
• W1981907708 cites W2049118022 @default.
• W1981907708 cites W2051654117 @default.
• W1981907708 cites W2057692022 @default.
• W1981907708 cites W2061817607 @default.
• W1981907708 cites W2063721875 @default.
• W1981907708 cites W2073714240 @default.
• W1981907708 cites W2073879622 @default.
• W1981907708 cites W2074768610 @default.
• W1981907708 cites W2075468840 @default.
• W1981907708 cites W2075701764 @default.
• W1981907708 cites W2078022887 @default.
• W1981907708 cites W2079769193 @default.
• W1981907708 cites W2080871860 @default.
• W1981907708 cites W2081167734 @default.
• W1981907708 cites W2083624153 @default.
• W1981907708 cites W2087183253 @default.
• W1981907708 cites W2092956715 @default.
• W1981907708 cites W2094779443 @default.
• W1981907708 cites W2102537419 @default.
• W1981907708 cites W2102697248 @default.
• W1981907708 cites W2103636724 @default.
• W1981907708 cites W2106140689 @default.
• W1981907708 cites W2107029002 @default.
• W1981907708 cites W2109645680 @default.
• W1981907708 cites W2111120490 @default.
• W1981907708 cites W2114926334 @default.
• W1981907708 cites W2128122374 @default.
• W1981907708 cites W2152403153 @default.
• W1981907708 cites W2155524113 @default.
• W1981907708 cites W2337120805 @default.
• W1981907708 cites W4211027922 @default.
• W1981907708 cites W4253858704 @default.
• W1981907708 doi "https://doi.org/10.1002/prot.340160303" @default.
• W1981907708 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/8346190" @default.
• W1981907708 hasPublicationYear "1993" @default.
• W1981907708 type Work @default.
• W1981907708 sameAs 1981907708 @default.
• W1981907708 citedByCount "212" @default.
• W1981907708 countsByYear W19819077082012 @default.
• W1981907708 countsByYear W19819077082013 @default.
• W1981907708 countsByYear W19819077082014 @default.
• W1981907708 countsByYear W19819077082015 @default.
• W1981907708 countsByYear W19819077082016 @default.
• W1981907708 countsByYear W19819077082017 @default.
• W1981907708 countsByYear W19819077082018 @default.
• W1981907708 countsByYear W19819077082019 @default.
• W1981907708 countsByYear W19819077082020 @default.
• W1981907708 countsByYear W19819077082021 @default.
• W1981907708 countsByYear W19819077082022 @default.
• W1981907708 countsByYear W19819077082023 @default.
• W1981907708 crossrefType "journal-article" @default.
• W1981907708 hasAuthorship W1981907708A5033385040 @default.
• W1981907708 hasAuthorship W1981907708A5086615420 @default.
• W1981907708 hasConcept C112887158 @default.
• W1981907708 hasConcept C121332964 @default.
• W1981907708 hasConcept C125888099 @default.
• W1981907708 hasConcept C126061179 @default.
• W1981907708 hasConcept C141780669 @default.
• W1981907708 hasConcept C147597530 @default.
• W1981907708 hasConcept C159467904 @default.
• W1981907708 hasConcept C162641036 @default.
• W1981907708 hasConcept C178790620 @default.
• W1981907708 hasConcept C184779094 @default.

• next