Efficient Computation of Three-dimensional Protein Structures in Solution from Nuclear Magnetic Resonance Data Using the Program DIANA and the Supporting Programs CALIBA, HABAS and GLOMSA

Güntert, Peter; Braun, Werner; Wüthrich, Kurt

doi:10.1142/9789812795830_0037

Cited by 181 publications

(286 citation statements)

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“…NOESY cross-peak intensities were converted into upls and lols using the program CALIBA (Gu È ntert et al, 1991) with the modi®cation that pseudo-atom corrections are set negative for lols. The atoms and the pseudo-atoms of the non-standard fragments used in the calculations (see the next section for details) were introduced into the program.…”

Section: Calculation Of Restraintsmentioning

confidence: 99%

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

Messias

Kastrau

Costa

et al. 1998

Journal of Molecular Biology

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Desulfovibrio vulgaris cytochrome c 3 is a 14 kDa tetrahaem cytochrome that plays a central role in energy transduction. The three-dimensional structure of the ferrocytochrome at pH 8.5 was solved through twodimensional 1 H-NMR. The structures were calculated using a large amount of experimental information, which includes upper and lower distance limits as well as dihedral angle restraints. The analysis allows for fast-¯ipping aromatic residues and¯exibility in the haem plane. The structure was determined using 2289 upper and 2390 lower distance limits, 63 restricted ranges for the f torsion angle, 88 stereospeci®c assignments out of the 118 stereopairs with non-degenerate chemical shifts (74.6%), and 115 out of the 184 nuclear Overhauser effects to fastipping aromatic residues (62.5%), which were pseudo-stereospeci®cally assigned to one or the other side of the ring. The calculated NMR structures are very well de®ned, with an average root-mean-square deviation value relative to the mean coordinates of 0.35 A Ê for the backbone atoms and 0.70 A Ê for all heavy-atoms. Comparison of the NMR structures of the ferrocytochrome at pH 8.5 with the available X-ray structure of the ferricytochrome at pH 5.5 reveals that the general fold of the molecule is very similar, but that there are some distinct differences. Calculation of ring current shifts for the residues with signi®cantly different conformations con®rms that the NMR structures represent better its solution structure in the reduced form. Some of the localised differences, such as a reorientation of Thr24, are thought to be state-dependent changes that involve alterations in hydrogen bond networks. An important rearrangement in the vicinity of the propionate groups of haem I and involving the covalent linkage of haem II suggests that this is the critical region for the functional cooperativities of this protein. # 1998 Academic PressKeywords: multihaem cytochrome; NMR structure; ring current shifts; redox-Bohr effect; cooperativity *Corresponding author IntroductionThe functional cooperativity between different regions of certain proteins is a fundamental property for controlling and coordinating important chemical events in the living cell. Although the molecular basis for the ®ne regulation of several types of cooperativity mechanisms has been E-mail address of the corresponding author: xavier@itqb.unl.pt Abbreviations used: DvHc 3 , Desulfovibrio vulgaris (Hildenborough) cytochrome c 3 ; NMR, nuclear magnetic resonance; 2D, two-dimensional; 2D-1 H-NMR, two-dimensional proton NMR; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser spectroscopy; COSY, correlation spectroscopy; DQF-COSY, double-quantum ®ltered COSY; TOCSY, total correlation spectroscopy; TPPI, time-proportional phase incrementation; ppm, parts per million; DSS, 2,2-dimethyl-2-silapentane-5-sulfonate; MD, molecular dynamics; RMSD, root-mean-square deviation; lol, lower distance limit; upl, upper distance limit.0022±2836/98/340719±21 $30.00/0 # 1998 Academic Press successfully established ...

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Section: Calculation Of Restraintsmentioning

confidence: 99%

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

Messias

Kastrau

Costa

et al. 1998

Journal of Molecular Biology

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“…The program DIANA (Giintert et al, 1991) was used to identify and remove redundant structure information. Subsequently, the standard protocol in X-PLOR 3.1 (Briinger, 1992) for protein structure calculations was applied using, first, distance geometry; second, 3 ps of simulated annealing at 2,000 K, followed by 5 ps of simulated annealing while cooling to 100 K (Nilges et al, 1988) in the simulated annealing procedure; and third, 4.7 ps of simulated annealing while cooling from 1,000 K to 100 K in the refinement procedure.…”

Section: Structure Calculationsmentioning

confidence: 99%

Structure in solution of a four‐helix lipid binding protein

et al. 1996

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Because of the low solubility of lipids in water, intercellular and intracellular pathways of lipid transfer are necessary, e.g., for membrane formation. The mechanism by which lipids in vivo are transported from their site of biogenesis (endoplasmatic reticulum and the chloroplasts) to their place of action is unknown. Several small plant proteins with the ability to mediate transfer of radiolabeled phospholipids in vitro from liposomal donor membranes to mitochondrial and chloroplast acceptor membranes have been isolated, and a protein with this ability, the nonspecific lipid transfer protein (nsLTP) isolated from barley seeds (bLTP), has been studied here. The structure and the protein lipid interactions of lipid transfer proteins are relevant for the understanding of their function, and here we present the three-dimensional structure in solution of bLTP as determined by NMR spectroscopy. The ' H NMR spectrum of the 91-residue protein was assigned for more than 97% of the protein ' H atoms, and the structure was calculated on the basis of 813 distance restraints from 'H-'H nuclear Overhauser effects, four disulfide bond restraints, from dihedral angle restraints for 66 @-angles, 61 x' angles, and 2 x ' angles, and from 31 sets of hydrogen bond restraints. The solution structure of bLTP consists of four well-defined a-helices A-D (A, Cys 3-Gly 19; B, Gly 25-Ala 38; C, Arg 44-Gly 57; D, Leu 63-Cys 73), separated by three short loops that are less well defined and concluded by a well defined C-terminal peptide segment with no observable regular secondary structure. For the 17 structures that are used to represent the solution structure of bLTP, the RMS deviation to an average structure is 0.63 A f 0.04 A for backbone atoms and 0.93 A k 0.06 A for all heavy atoms. The secondary structure elements and their locations in the sequence resemble those of nsLTP from two other plant species, wheat and maize, whose structures were previously determined (Gincel E et al, 1995, Eur JBiochern 226:413-422; Shin DH et al, 1995, Structure3: 189-199). In bLTP, the residues analogous to those in maize nsLTP that constitute the palmitate binding site are forming a similar hydrophobic cavity and a potential acyl group binding site. Analysis of the solution structure of bLTP and bLTP in complex with a ligand might provide information on the conformational changes in the protein upon ligand binding and subsequently provide information on the mode of ligand uptake and release. In this work, we hope to establish a foundation for further work of determining the solution structure of bLTP in complex with palmitoyl coenzyme A, which is a suitable ligand, and subsequently to outline the mode of ligand binding.

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“…The structure of the BID protein was defined based on ~1700 NMR-derived distance constraints. This included 1350 structurally relevant NOE-based constraints, 275 dihedral angle constraints measured from J-coupling constants and local bond geometry (Guntert et al, 1991), and constraints from 56 hydrogen bonds implied by hydrogen-deuterium exchange experiments and local secondary structure. This corresponds to an average density of ~15 constraints per residue in all regions of secondary structure.…”

Section: Structure Determination Of Bidmentioning

confidence: 99%

Rational Design of Regulators of Programmed Cell Death in Human Breast Cancer

Cowburn¹

2003

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Efficient Computation of Three-dimensional Protein Structures in Solution from Nuclear Magnetic Resonance Data Using the Program DIANA and the Supporting Programs CALIBA, HABAS and GLOMSA

Cited by 181 publications

References 0 publications

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

Structure in solution of a four‐helix lipid binding protein

Rational Design of Regulators of Programmed Cell Death in Human Breast Cancer

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