Theoretical study of arginine–carboxylate interactions

Melo, André; Ramos, María J.; Floriano, Wely B.; Gomes, J.A.N.F.; Leão, J.F.R.; Magalhães, Alexandre L.; Maigret, Bernard; Nascimento, M. C.; Reuter, Nathalie

doi:10.1016/s0166-1280(98)00396-0

Cited by 41 publications

(37 citation statements)

References 35 publications

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“…The validity of this type of approaches has been demonstrated before in the mechanistic study of FTase 34,35 and of several different enzymes. [44][45][46][47][48][49][50] The model was prepared starting from the 1KZP structure, 40 a crystallographic structure of the FTase product complex (resolution 2.10 Å ).…”

Section: Smaller Modelmentioning

confidence: 99%

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere

2007

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Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co(2+)-substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested.

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Section: Smaller Modelmentioning

confidence: 99%

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere

2007

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“…Guanidinium ions have long been utilized in modelling Arg-Glu or Arg-Asp side-chain interactions in proteins (see, for example, Melo et al, 1999;Fü lscher & Mehler, 1988;Singh et al, 1987). More recently, the same types of interaction have been utilized in host-guest and sensor chemistry (see, for example, Houk et al, 2005) and in crystal engineering (see, for example, Holman et al, 2001;Burrows et al, 2003).…”

Section: Commentmentioning

confidence: 99%

Tetrakis(guanidinium) butane-1,2,3,4-tetracarboxylate

McKee

Najafpour²

2007

Acta Cryst E

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“…18,19,20 The energetics of 2.5 and 2.6 (where R 1 = R 2 = CH 3 ) were calculated at the RHF/6-31G** and MP2/6-31G** abinitio level. 18 Semi-empirical results obtained with AM1 qualitatively reproduced the abinitio results and both levels of theory predict that 2.5 is not likely to exist in the gas phase, with 2.6 being energetically favored by ~18 kJ/mol at the highest level of theory. …”

Section: 6mentioning

confidence: 99%

Salt Bridge Stabilization of Charged Zwitterionic Arginine Aggregates in the Gas Phase

2001

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Portions previously published in: Julian R. R.; Hodyss R.; Beauchamp J. L. J. Am. Chem. Soc. 2001, 123, 3577-3583. IntroductionAmino acids are known to exist as zwitterions in solution, but conditions appropriate for stabilization of the zwitterionic form in the gas phase remain debatable. Studies of the gas phase acidity and basicity of glycine with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry have shown that the glycine zwitterion is unstable by ~84 kJ/mol. 1 Many recent calculations confirm that glycine is unlikely to exist in the gas phase as a zwitterion; 2 furthermore, the zwitterion is not even predicted to be a minima on the potential energy surface. Theory suggests that water molecules can stabilize the zwitterionic form of glycine in the gas phase, with recent calculations suggesting that two water molecules are required. 3 In contrast, recent experimental results suggest that the number of water molecules necessary to stabilize glycine as a zwitterion is five. The gas phase stability of the zwitterionic form of arginine is predicted to be much more favorable. The arginine zwitterion is created by transferring a proton from the Cterminus to the side chain (see 2.1 and 2.2). The nomenclature indicated for arginine structures 2.1-2.4 will be used in the present work. Arginine is the most basic amino acid (see Table 2.1). This high basicity increases the stability of zwitterionic arginine in the gas phase relative to other amino acids. However, recent experiments have shown that isolated arginine is not a zwitterion. Cavity-ring down laser absorption spectra of jetcooled arginine do not exhibit a peak corresponding to the calculated carboxylate asymmetric stretch of the zwitterion. 5 High level computations have confirmed that arginine (2.1) is more stable than zwitterionic arginine (2.2) in the absence of an 18 additional charge. 6 However, theory predicts that the zwitterionic arginine is only less stable than arginine by 4-12 kJ/mol, depending on the level of theory.6

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Theoretical study of arginine–carboxylate interactions

Cited by 41 publications

References 35 publications

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere

Tetrakis(guanidinium) butane-1,2,3,4-tetracarboxylate

Salt Bridge Stabilization of Charged Zwitterionic Arginine Aggregates in the Gas Phase

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