Charge Invariant Protein–Water Relaxation in GB1 via Ultrafast Tryptophan Fluorescence
19 Feb 2014-Journal of the American Chemical Society (American Chemical Society)-Vol. 136, Iss: 7, pp 2739-2747
TL;DR: The protein–water interface is a critical determinant of protein structure and function, yet the precise nature of dynamics in this complex system remains elusive, and molecular dynamics simulations reveal a balancing, sometimes even countervailing influence of protein and water dipoles.
Abstract: The protein–water interface is a critical determinant of protein structure and function, yet the precise nature of dynamics in this complex system remains elusive. Tryptophan fluorescence has become the probe of choice for such dynamics on the picosecond time scale (especially via fluorescence “upconversion”). In the absence of ultrafast (“quasi-static”) quenching from nearby groups, the TDFSS (time-dependent fluorescence Stokes shift) for exposed Trp directly reports on dipolar relaxation near the interface (both water and polypeptide). The small protein GB1 contains a single Trp (W43) of this type, and its structure is refractory to pH above 3. Thus, it can be used to examine the dependence of dipolar relaxation upon charge reconfiguration with titration. Somewhat surprisingly, the dipolar dynamics in the 100 fs to 100 ps range were unchanged with pH, although nanosecond yield, rates, and access all changed. These results were rationalized with the help of molecular dynamics (including QM-MM) simulation...
Citations
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
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TL;DR: An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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Additional excerpts
...[167] measured the TDFSS of a solvent-exposed tryptophan upon titration and observed constancy of the dipolar dynamics with charge variation....
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TL;DR: It is convincingly show that the water-protein relaxations are strongly coupled and the hydration water molecules govern such fluctuations on the picosecond time scales.
Abstract: The fluctuations of hydration water and the protein are coupled together at the protein surface and often such water–protein dynamic interactions are controlled presumably by hydration water motions. However, direct evidence is scarce and it requires measuring the dynamics of hydration water and protein side chain simultaneously. Here, we use a unique protein with a single tryptophan to directly probe interfacial water and related side chain relaxations with temperature dependence. With systematic mutations to change local chemical identity and structural flexibility, we found that the side chain relaxations are always slower than hydration water motions and the two dynamic processes are linearly correlated with the same energy barriers, indicating the same origin of both relaxations. The charge mutations change the rates of hydration water relaxations but not the relaxation barriers. These results convincingly show that the water–protein relaxations are strongly coupled and the hydration water molecules ...
32 citations
TL;DR: The results suggest that conformational rearrangements, from an induced fit model of substrate binding to HepI, are important for catalysis, and the disruption of these conformational dynamics may serve as a novel mechanism for inhibiting this and other glycosyltransferase enzymes.
Abstract: Heptosyltransferase I (HepI) catalyzes the addition of l-glycero-β-d-manno-heptose to Kdo2-Lipid A, as part of the biosynthesis of the core region of lipopolysaccharide (LPS). Gram-negative bacteria with gene knockouts of HepI have reduced virulence and enhanced susceptibility to hydrophobic antibiotics, making the design of inhibitors of HepI of interest. Because HepI protein dynamics are partially rate-limiting, disruption of protein dynamics might provide a new strategy for inhibiting HepI. Discerning the global mechanism of HepI is anticipated to aid development of inhibitors of LPS biosynthesis. Herein, dynamic protein rearrangements involved in the HepI catalytic cycle were probed by combining mutagenesis with intrinsic tryptophan fluorescence and circular dichroism analyses. Using wild-type and mutant forms of HepI, multiple dynamic regions were identified via changes in Trp fluorescence. Interestingly, Trp residues (Trp199 and Trp217) in the C-terminal domain (which binds ADP-heptose) are in a mor...
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TL;DR: Using femtosecond fluorescence upconversion, it is shown that this molecule in solution participates in ultrafast self-quenching along with both bulk solvent relaxation and spectral relaxation on 1.4 and 26 ps timescales.
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References
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
TL;DR: A review of the use of the technique of solute fluorescence quenching to study the structure and dynamics of proteins and a number of factors are discussed that must be considered in analyzing such data.
1,644 citations
TL;DR: This study predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins using a hybrid quantum mechanical-classical molecular dynamics method with the assumption that only electrostatic interactions of thetryptophan ring electron density with the surrounding protein and solvent affect the transition energy.
1,239 citations
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Abstract: 1. VITAMIN B1 (THIAMINE MONONITRATE) 20% w/w 2. VITAMIN B2 (RIBOFLAVIN) 10% w/w 3. VITAMIN B3 (NICOTINAMIDE) 50% w/w 4. VITAMIN B5 (CALCIUM PANTOTHENATE) 10% w/w 5. VITAMIN B6 (PYRIDOXAL 5 PHOSPHATE) 10% w/w 6. VITAMIN B7 (BIOTIN) 1% w/w 7. VITAMIN B9 (FOLIC ACID) 3% w/w 8. VITAMIN B 12(COBALAMINS) 1.2% w/w 9. VITAMIN C (ASCORBIC ACID) 45% w/w 10. VITAMIN D3 (CHOLECALCIFEROL) 500 IU/MG 11. VITAMIN E (ALPHA TOCOPHEROL) 50% w/w 12. VITAMIN K (PHYLLOQUINONE) 0.1% w/w 13. VITAMIN A ACETATE 14. VITAMIN A PALMITATE
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TL;DR: The results point to the existence of a first hydration shell with an average density approximately 10% larger than that of the bulk solvent in the conditions studied, which suggests that this may be a general property of aqueous interfaces.
Abstract: The structure of the protein–solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein–solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density ≈10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.
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