Importance of Structural Tightening, as Opposed to Partially Bound States, in the Determination of Chemical Shift Changes at Noncovalently Bonded Interfaces

Williams, Dudley H.; Davies, Nichola L.; Koivisto, Jari

doi:10.1021/ja047198y

Cited by 10 publications

(12 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Upon introduction of further interactions, the balance shifts toward more frequent formation of the interactions and less mobility. There is experimental evidence for both the structural tightening model(26) and the model of partially bound states(27) in different systems. Since proteins bind ligands in many geometric arrangements ranging from loosely surface-bound to deeply buried, it is likely that both are valid in different contexts.…”

Section: General Design Aspectsmentioning

confidence: 99%

A Medicinal Chemist’s Guide to Molecular Interactions

2010

View full text Add to dashboard Cite

Section: General Design Aspectsmentioning

confidence: 99%

A Medicinal Chemist’s Guide to Molecular Interactions

2010

View full text Add to dashboard Cite

“…109 This issue has been extensively studied experimentally by Williams et al [110][111][112] and forms the theoretical basis of fragment-based drug discovery, 113 as exemplified in ''SAR by NMR.'' 114 Mammen et al 115 developed a classical model for estimating the entropy of torsional motion about a single bond.…”

Section: Torsional Entropymentioning

confidence: 99%

Back to the future: Ribonuclease A

2008

View full text Add to dashboard Cite

Pancreatic ribonuclease A (EC 3.1.27.5, RNase) is, perhaps, the best‐studied enzyme of the 20th century. It was isolated by René Dubos, crystallized by Moses Kunitz, sequenced by Stanford Moore and William Stein, and synthesized in the laboratory of Bruce Merrifield, all at the Rockefeller Institute/University. It has proven to be an excellent model system for many different types of experiments, both as an enzyme and as a well‐characterized protein for biophysical studies. Of major significance was the demonstration by Chris Anfinsen at NIH that the primary sequence of RNase encoded the three‐dimensional structure of the enzyme. Many other prominent protein chemists/enzymologists have utilized RNase as a dominant theme in their research. In this review, the history of RNase and its offspring, RNase S (S‐protein/S‐peptide), will be considered, especially the work in the Merrifield group, as a preface to preliminary data and proposed experiments addressing topics of current interest. These include entropy–enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action. In continuing to use RNase as a prototypical enzyme, we stand on the shoulders of the giants of protein chemistry to survey the future. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 259–277, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

show abstract

“…The binding between two molecules V to give dimer V‐V is deemed to be cooperative in a positive sense with respect to the ligand L, if the equilibrium constant of the complex LV–VL is greater than the constant for dimerization V + V→ V‐V10. As examples, we note that cooperative binding is a feature of DNA duplexes, polypeptide systems, ion pairing, GAs, and others12, 13. Most cooperative effects are understood in terms of enthalpy changes in the molecular conformation.…”

Section: Introductionmentioning

confidence: 97%

Dimerization free energy of vancomycin‐group antibiotics and the cooperative effect: A density functional approach

Lee

Sagui

Roland

2010

Int J of Quantum Chemistry

View full text Add to dashboard Cite

ABSTRACT:The cooperative effects between the binding of model bacterial cell wall termini and the dimer forms of the glycopeptide antibiotic vancomycin and chloroeremomycin were investigated with conventional and divide-and-conquer (DC) ab initio quantum chemistry simulations. This feature is potentially important for drug design and controlling molecular recognition phenomena in these and other biochemical systems. In terms of the calculation, the vibrational contributions to the dimerization free energies of both molecules found to be the most costly and necessitated the use of the DC method. We specifically focused on calculating the relative strength of the cooperative effect for the two antibiotics. In good agreement with experiments, we find that the cooperative effect is stronger for chloro-eremomycin by about 1.39 kcal/mol.

show abstract

Importance of Structural Tightening, as Opposed to Partially Bound States, in the Determination of Chemical Shift Changes at Noncovalently Bonded Interfaces

Cited by 10 publications

References 26 publications

A Medicinal Chemist’s Guide to Molecular Interactions

A Medicinal Chemist’s Guide to Molecular Interactions

Back to the future: Ribonuclease A

Dimerization free energy of vancomycin‐group antibiotics and the cooperative effect: A density functional approach

Contact Info

Product

Resources

About