Arginine–phosphate salt bridges in protein–DNA complexes: a Car–Parrinello study

Frigyes, Dávid; Alber, Frank; Pongor, Sándor; Carloni, Paolo

doi:10.1016/s0166-1280(01)00368-2

Cited by 35 publications

(32 citation statements)

References 38 publications

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“…Based on a molecular dynamics study, it has been proposed that hydration of a bidentate complex of the Arg guanidino group significantly increases the polarity of the N-H bonds with a subsequently increased positive charge at each N-H hydrogen which can interact with the oxygen in water. 56 Additionally, the modification to DHCH-Arg allows a protrusion of the surface Arg residues to the surrounding hydration shell, which is paralleled with an increase of the polarization of the electron shell around the guanidino terminus of DHCH-Arg. This interplay might facilitate the accessibility of the RBD for polyP.…”

Section: Papermentioning

confidence: 99%

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

et al. 2020

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Section: Papermentioning

confidence: 99%

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

et al. 2020

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“…It has been revealed from crystal structures that the major coordination partners are Lys and Arg side chains. On the DNA side, important recognition motifs are hydrogen bonds or electrostatic interactions (salt bridges) involving the DNA phosphate groups as hydrogen‐bond acceptors, but also the ribose or the base moieties . We previously established that in DnaB from H. pylori , the ATP hydrolysis transition state, mimicked by ADP:AlF 4 − , preorganizes the helicase for binding single‐stranded DNA to the C‐terminal domain (CTD) .…”

Section: Figurementioning

confidence: 99%

“…[9] Intermolecular information can also be obtained from 31 P-detected, heteronuclear correlation experimentsp robingt he spatial proximity of nucleotide 31 Pa nd protein 15 No r 13 Cn uclei. On the DNA side, important recognition motifs are hydrogen bonds or electrostatic interactions (salt bridges) [40][41][42][43] involving the DNA phosphate groupsa sh ydrogen-bond acceptors, but also the ribose or the base moieties. [14][15][16][17][18][19][20][21][22][23] Proton chemical-shift values are highly sensitivet oh ydrogen bonding [24][25][26][27] as shown in theoretical, [26,27] buta lso in experimental studies.…”

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Nucleotide Binding Modes in a Motor Protein Revealed by ³¹P‐ and ¹H‐Detected MAS Solid‐State NMR Spectroscopy

et al. 2019

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Protein-nucleic acidi nteractions play important roles not only in energy-providing reactions,s uch as ATPh ydrolysis, but also in reading, extending, packaging, or repairing genomes. Althought hey can often be analyzed in detail with X-ray crystallography, complementary methods are neededt ov isualize them in complexes, which are not crystalline. Here, we show how solid-stateN MR spectroscopy can detecta nd classify protein-nucleic interactions through site-specific 1 H-and 31 P-detected spectroscopicm ethods. The sensitivity of 1 Hc hemicalshift values on noncovalent interactions involved in these molecular recognition processes is exploiteda llowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecamericD naB helicasei nc omplex with ADP:AlF 4 À :DNA, and this despite the very challenging size of the complex.Nucleotide-protein interactions playacentral role in two major biological functions:i ne nergy-providing reactions, where ATPi sh ydrolyzed to yield energy to motor domains driving reactions [1,2] and in interactions with RNA or DNA, central in al arge variety of biomolecular functions. Binding of nucleotides, such as ATPa nd DNA, occurs throughn oncovalent interactions includingh ydrogen bonds, electrostatic (salt bridges), and van der Waals interactions [3,4] (the latter also comprising interactions between aromatic rings [5] ). These interactions have been typicallys tudied in the past by high-resolution X-ray crystallography. [4,6,7] Still, many of the scenarios described above involve protein complexes, which are difficult to crystallize, and when they do so, might reflect at insufficient resolution to clearly identify interactions.A lternative methods are therefore neededa nd can be providedt hrough solid-state NMR spectroscopy,w hich can access also large biomolecular complexes,a nd importantly in sample formats where the assemblies are simply sedimented into the NMR rotor. [8] And indeed, solid-state NMR spectroscopy has been used to identify residues at protein-RNA interfaces in smaller proteins. [9][10][11][12] Twoa pproaches are particularly promising to probe nucleotide interactions:p hosphorus-( 31 P) and proton-( 1 H) detected spectroscopy.D istances between 31 Ps pins of DNA and 15 N spins of ap rotein have been measuredb yu sing transferredecho, double-resonance (TEDOR) experiments. [9] Intermolecular information can also be obtained from 31 P-detected, heteronuclear correlation experimentsp robingt he spatial proximity of nucleotide 31 Pa nd protein 15 No r 13 Cn uclei. [9,13] Proton-detected solid-state NMR spectroscopy at fast MAS frequencies has emerged in the last years and needs today only af ew hundred micrograms of fully protonated protein sample. [14][15][16][17][18][19][20][21][22][23] Proton chemical-shift values are highly sensitivet oh ydrogen bonding [24][25][26][27] as shown in theoretical, [26,27] ...

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“…According to a systematic geometric analysis of the Brookhaven Protein Data Bank, the stereochemistry of the side-chain H-bonds of proteins was pointed out to be characterized by at least three factors: (a) the electronic configuration of the H-bond acceptor atoms, (b) the steric accessibility of the H-bond donor atoms, and (c) the conformation of amino acid side-chains. 27 There have also been a number of theoretical studies aimed at quantifying the strength of interaction of small ions, 9,15,26,[28][29][30][31][32][33][34][35][36][37] mimicking the salt bridges between the CO − 2 side group of glutamate or asparate and the guanidinium side group of the arginine. In particular, the interaction energy in the Arg-Glu salt bridge varies from 35 [45][46][47][48][49] The IR spectrum was evaluated in some papers; 45,49 however, the 2000-2800 frequency region was not considered.…”

Section: Introductionmentioning

confidence: 99%

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

Vener

Odinokov

Wehmeyer

et al. 2015

The Journal of Chemical Physics

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Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.

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Arginine–phosphate salt bridges in protein–DNA complexes: a Car–Parrinello study

Cited by 35 publications

References 38 publications

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

Nucleotide Binding Modes in a Motor Protein Revealed by ³¹P‐ and ¹H‐Detected MAS Solid‐State NMR Spectroscopy

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

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Arginine–phosphate salt bridges in protein–DNA complexes: a Car–Parrinello study

Cited by 35 publications

References 38 publications

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

Nucleotide Binding Modes in a Motor Protein Revealed by 31P‐ and 1H‐Detected MAS Solid‐State NMR Spectroscopy

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

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Nucleotide Binding Modes in a Motor Protein Revealed by ³¹P‐ and ¹H‐Detected MAS Solid‐State NMR Spectroscopy