Molecular Fragment Replacement Approach to Protein Structure Determination by Chemical Shift and Dipolar Homology Database Mining

Kontaxis, Georg; Delaglio, Frank; Bax, Ad

doi:10.1016/s0076-6879(05)94003-2

Cited by 57 publications

(95 citation statements)

References 77 publications

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“…The A53T substitution has no adverse effect on helix stability, neither on a sub-nanosecond nor on a nano-to microsecond timescale. In fact, increased 13 C ␣ secondary shifts relative to wild type for Thr 53 -Thr 54 indicate a small increase in local helical character at the site of mutation. This observation is interesting in light of the fact that a substitution of Thr for Ala is often a destabilizing ␣-helical conformation (77).…”

Section: Discussionmentioning

confidence: 97%

“…Structure Calculation-In complete analogy to the aS wild-type structure calculation (20), backbone dihedral angle restraints were derived by molecular fragment replacement (MFR) (53,54). Considering that large amplitude internal dynamics complicates such an analysis, MFR results are restricted to residues exhibiting generalized order parameters, S 2 , above 0.6.…”

Section: Methodsmentioning

confidence: 99%

“…The unusually strong intermediate timescale dynamics of the aSmicelle system make the structure calculation of the aS(A30P) variant particularly difficult. Although information on the secondary structure elements present was obtained by MFR (53,54), it did not prove accurate for defining the complex tertiary structure of residues Glu 28 -Thr 44 . Thus, only an illustrative picture of the effective, average secondary structure of aS(A30P) can be given (Fig.…”

Section: Structure and Dynamics Of As(a53t) Are Essentially Indistingmentioning

confidence: 99%

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Comparison of Structure and Dynamics of Micelle-bound Human α-Synuclein and Parkinson Disease Variants

Ulmer

Bax

2005

Journal of Biological Chemistry

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149

165

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Three point mutations (A30P, E46K, and A53T) as well as gene triplication genetically link the 140-residue protein ␣-synuclein (aS) to the development of Parkinson disease. Here, the structure and dynamics of micelle-bound aS(A30P) and aS(A53T) are described and compared with wild-type aS, in addition to describing the aS-micelle interaction. A53T is sensed only by directly adjacent residues and leaves the backbone structure and dynamics indistinguishable from the wild type. A30P interrupts one helix turn (Val 26 -Ala 29 ) and destabilizes the preceding one. A shift in helix register following A30P disturbs the canonical succession of polar and hydrophobic residues for at least two turns. The shortened helix-N adopts a slightly higher helical content and is less bent, indicating that strain was present in the micelle-bound helix. In the vicinity of the A30P-induced perturbations, the underlying micelle environment has rearranged, but nevertheless all aS variants maintain similar interrelationships with the micelle. Moreover, aS-micelle immersion correlates well with fast and slow aS backbone dynamics, allowing a rare insight into protein-micelle interplay.Parkinson disease (PD) 3 is characterized by the selective demise of neurons of the substantia nigra pars compacta, leading to progressive motoric dysfunction (1-3). Cell death occurs as a result of the accumulation of intraneuronal inclusions known as Lewy bodies (ubiquinated protein deposits in the cytoplasm) and Lewy neurites (thread-like proteinaceous inclusions within neurites). Biochemical and histological analyses have identified the 140-residue protein ␣-synuclein (aS) to be a major component of Lewy bodies and Lewy neurites (4, 5). Furthermore, aS gene triplication as well as any of the mutations A30P, E46K, and A53T have been genetically linked to familial PD (6 -9). At the molecular level, misfolding of aS into aggregates appears to be a common denominator in the pathogenesis of PD, which strongly correlates with age. Misfolding benefits from the impaired degradation of aS (10) and, in particular, oxidation of aS by reactive oxygen species (11,12) created by impairments in mitochondrial complex I activity (11), caused, for example, by environmental toxins, and catalyzed by iron and copper. Moreover, the dopamine-containing neurons of the substantia nigra pars compacta exhibit a unique sensitivity to impairments in mitochondrial complex I activity (11).In aqueous solution aS is predominantly unfolded but readily associates with small unilamellar vesicles (SUV) and micelles containing negatively charged lipids and detergents, respectively (13-16), supporting its association with presynaptic vesicles in vivo and rationalizing its localization primarily at axon termini (17, 18). In complex with SUV of 300 -400 Å diameter, the repeat region of aS ( Fig. 1) is likely to form a single, uninterrupted ␣-helix (19), whereas in complex with smaller diameter micelles the repeat region is partitioned into two anti-parallel ␣-helices, helix-N (Val 3 -Val 37 ) an...

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Section: Discussionmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Section: Structure and Dynamics Of As(a53t) Are Essentially Indistingmentioning

confidence: 99%

See 1 more Smart Citation

Comparison of Structure and Dynamics of Micelle-bound Human α-Synuclein and Parkinson Disease Variants

Ulmer

Bax

2005

Journal of Biological Chemistry

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149

165

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“…The recently described chemical-shift-based Rosetta (CS-Rosetta) procedure 17,25 generates protein structures in much the same way as standard Rosetta but uses the MFR program 26 to select its fragments on the basis of chemical shifts observed in the protein of unknown structure. After Rosetta generation of low-energy protein models, based on these starting fragments, agreement between chemical shifts predicted for each of these Rosetta models by the program SPARTA 27 and experimental values is used to add a pseudoenergy term to the standard Rosetta energy, which is then used for selecting viable models.…”

mentioning

confidence: 99%

De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds

Shen

Bryan

et al. 2010

Protein Science

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Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA 95 ) and an a/b-fold protein (GB 95 ), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA 95

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“…the PDB) for homologous structures that allow close reproduction of the measured RDCs [247]. RDC-based molecular fragment replacement is conceptually similar but more generally applicable [248][249][250]. All measured one-bond backbone RDCs within a sliding frame of usually 7 to 10 residues are fitted against synthetic RDCs of all fragment structures in a comprehensive database.…”

Section: Residual Dipolar Couplings Provide Global Structure Restraintsmentioning

confidence: 99%

Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules

Stangler¹,

Hartmann²,

Willbold³

et al. 2006

Zeitschrift für Physikalische Chemie

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Solution NMR / Structure / Dynamics / InteractionsHigh resolution liquid state nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for in vitro studies of structure and dynamics of soluble biological macromolecules under physiological conditions. The unique combination of atomically resolved structural data with both local and global dynamic features covering the entire range of time scales from picoseconds to seconds makes NMR the method of choice in a very diverse and rapidly growing array of biochemical, biomedical, and pharmaceutical applications. After briefly introducing the basic principles of liquid state NMR we review recent methodological and instrumental advances in the field of biologically focused high resolution NMR. The main emphasis of the second part is on molecular interactions. Such interactions are fundamental for the function of proteins in living systems, e.g. for signal transduction, enzymatic catalysis, and immune defense. The tremendous opportunities of high resolution NMR in the identification and detailed characterization of the sites and modes of molecular interactions will be demonstrated.

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Molecular Fragment Replacement Approach to Protein Structure Determination by Chemical Shift and Dipolar Homology Database Mining

Cited by 57 publications

References 77 publications

Comparison of Structure and Dynamics of Micelle-bound Human α-Synuclein and Parkinson Disease Variants

Comparison of Structure and Dynamics of Micelle-bound Human α-Synuclein and Parkinson Disease Variants

De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds

Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules

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