Water–protein interactions from high–resolution protein crystallography

Nakasako, Masayoshi

doi:10.1098/rstb.2004.1498

Cited by 164 publications

(135 citation statements)

References 65 publications

(121 reference statements)

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“…Despite its importance, gaining insight into the molecular mechanisms and structures of hydration water has been challenging and has led to conflicting descriptions, mainly due to its dynamic nature, which can be affected by various factors in the surrounding environment, including physicochemical properties of the solute molecules, as well as solvent composition, in particular, the presence of ions (4)(5)(6). High-resolution structural studies by x-ray crystallography or NMR, molecular dynamics (MD) simulations, solution scattering, and other biophysical studies have provided information on water-macromolecule interactions in specific systems (7)(8)(9)(10). NMR and neutron spectroscopy have revealed altered mobility of water molecules on protein surfaces with respect to the bulk (11)(12)(13)(14)(15), and time-resolved vibrational spectroscopy has revealed distinctive dynamics of solvation near the active sites of enzymes during catalysis with respect to bulk solvent (16).…”

Section: Introductionmentioning

confidence: 99%

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Kim

Martel

Girard

et al. 2016

Biophysical Journal

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Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (þ36, À6, and À29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.

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Section: Introductionmentioning

confidence: 99%

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Kim

Martel

Girard

et al. 2016

Biophysical Journal

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“…More recently, Nakasako (22) has also reported a large water network on the surface of a small killer toxin molecule from the halotolerant yeast Pichia farinosa, solved to 2.1 Å; this involves a total of 400 water molecules and 250 polar protein atoms and accounts for 90% of the total solvent. Rather than accumulate high The dependence of the water to protein residue ratio (ordinate) against the resolution in Å (abscissa) for the structure determinations of all proteins solved between 3.5-and 0.5-Å resolution.…”

Section: Analysis Of the Solvent Structure And Its Interaction With Tmentioning

confidence: 99%

Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei

Britton

Baker

Fisher

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

125

134

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The structure of glucose dehydrogenase from the extreme halophile Haloferax mediterranei has been solved at 1.6-Å resolution under crystallization conditions which closely mimic the ''in vivo'' intracellular environment. The decoration of the enzyme's surface with acidic residues is only partially neutralized by bound potassium counterions, which also appear to play a role in substrate binding. The surface shows the expected reduction in hydrophobic character, surprisingly not from changes associated with the loss of exposed hydrophobic residues but rather arising from a loss of lysines consistent with the genome wide-reduction of this residue in extreme halophiles. The structure reveals a highly ordered, multilayered solvation shell that can be seen to be organized into one dominant network covering much of the exposed surface accessible area to an extent not seen in almost any other protein structure solved. This finding is consistent with the requirement of the enzyme to form a protective shell in a dehydrating environment.Archaea ͉ x-ray structure ͉ water structure ͉ hydrophobic surface ͉ surface lysines

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“…2B). It is known that water molecules can form an intricate network that makes antibody-antigen interfaces fully complementary (36,37). Additionally, the side chain of M2-Glu8 interacts with those of Asn55 and Asn57 of the HCDR2 through water molecules, and its main-chain oxygen interacts with the mainchain nitrogen of Tyr100 of LCDR 3, again through a water molecule (Fig.…”

Section: Structure Of M2e In Complex With Mab 65mentioning

confidence: 99%

Structure of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus in Complex with a Protective Monoclonal Antibody

Cho

Schepens

Seok

et al. 2015

J Virol

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The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. IMPORTANCEM2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2. Matrix protein 2 (M2) is a structural protein of influenza A viruses and plays an important role in the virus life cycle. This type III membrane protein of 96 amino acid residues has an N-terminal ectodomain (M2e) of 23 residues, a transmembrane domain of 19 residues, and a cytoplasmic domain of 54 residues (1). M2 is classified as a viroporin. Mutational analysis and crystal and nuclear magnetic resonance (NMR) structural analysis of the M2 transmembrane domain revealed that it is composed of a fourstranded coiled coil and that two conserved amino acid residues (M2-His37 and -Trp41) have a key role in acid-induced proton gating (2-5). Following endocytosis of influenza A virions, the acidic endosomal environment activates the M2 channel so that protons enter the virion interior. The resulting acidification loosens the viral ribonucleoprotein complexes from matrix protein 1 (M1), which facilitates their migration through the membrane fusion pore into the host cell cytoplasm (6, 7). M2 can activate the inflammasome, impairs autophagosome maturation, and was recently shown to recruit parts of the autophagosome machinery to sites of virus budding by a conserved motif in its cytoplasmic domain (8, 9).The sequence of M2e is conserved and therefore has frequently been explored for the development of a universal influenza A vaccine (10-13). Immune protection by M2e-directed vaccines has been documented extensively in experimental animal models, including mice, ferrets, and swine (11-13). In addition, a phase I clinical study showed that M2e-based vaccines are safe and immunogenic in humans (10,14). Seasonal influenza A virus infection induces a poor immune responses to M2e, but this weak re...

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Water–protein interactions from high–resolution protein crystallography

Cited by 164 publications

References 65 publications

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei

Structure of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus in Complex with a Protective Monoclonal Antibody

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