The impact of structural genomics: the first quindecennial

Grabowski, M.; Niedzialkowska, E.; Zimmerman, Matthew; Minor, Władek

doi:10.1007/s10969-016-9201-5

Cited by 61 publications

(44 citation statements)

References 90 publications

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“…[27] It also furnishes the electron density, [27] which is denominated ρ value, of each bond critical point (BCP), which is the minimum of electron density in the bond path. The electronic density at the BCP may be a useful parameter for estimating hydrogen [28][29][30] and halogen interactions. [30] In this way, we assumed that the higher the electron density in BCP, the more stable is the considered bond.…”

Section: Resultsmentioning

confidence: 99%

[2]Rotaxanes Bearing a Tetralactam Macrocycle: The Role of a Trifurcated Hydrogen Bond in the Crystalline State

et al. 2019

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This study investigated the proper classification and quantification of intercomponent trifurcated hydrogen bonds, in the crystalline state, of rotaxanes bearing a tetralactam Leigh‐type macrocycle. Quantum mechanical calculations were carried out to obtain the interaction paths and their stabilization energies. In general, the use and necessity of fragmentation in types of interaction have been reported in the literature, although they are commonly performed only using a geometric approach. This results in N–H···O interactions that are indicated as the main interactions between components, neglecting other possible interactions. The use of energetic fragmentation was demonstrated here under an appropriate demarcation considering all interactions and showing the existence and role of the C–H···O interaction. The C–H···O interactions showed similar energy to N–H···O interactions with average values around –4.75 kcal mol–1 and –4.60 kcal mol–1, respectively. This revealed that the three hydrogen bonds are part of a cooperative set of interactions with a similar contribution. The trifurcated hydrogen bonds presented high contribution in the total intercomponent stabilization energy of the rotaxanes, with an average value of 51 % in the studied series.

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Section: Resultsmentioning

confidence: 99%

[2]Rotaxanes Bearing a Tetralactam Macrocycle: The Role of a Trifurcated Hydrogen Bond in the Crystalline State

et al. 2019

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“…Therefore, information on the protein structure has been suggested to improve the quality of sequence alignments, for the prediction of substrate specificities, and for the design of enzymes . As a consequence, large‐scale structural genomics projects sought to populate protein structure space …”

Section: Discussionmentioning

confidence: 99%

“…[40][41][42] As a consequence, large-scale structural genomics projects sought to populate protein structure space. 43 The annotation of ThDP-dependent decarboxylases is challenging, as demonstrated for the BFDC subfamily. 44 One possibility to improve on annotation by global sequence identity is genomic neighborhood analysis, as BFDC frequently occur with a (benz-)aldehyde dehydrogenase encoded in the genomic neighborhood.…”

Section: Comparison Of the Substrate Binding Sitementioning

confidence: 99%

Navigating within thiamine diphosphate‐dependent decarboxylases: Sequences, structures, functional positions, and binding sites

et al. 2019

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Thiamine diphosphate‐dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP‐dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP‐dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.

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Section: Introductionmentioning

confidence: 99%

“…Sequence databases are improving with regards to annotations [7,8] and coverage of protein domain space [9,10]. In addition, structural data is growing through structural genomics initiatives [11,12], further enabling large-scale homology modelling efforts [13,14].The accuracy of protein function prediction has improved over recent years as a result of better methods as well as increased experimentally-based annotations [15,16]. Most proteins predicted from genomes can now be at least partially annotated [17] through detected homology to existing proteins (e.g., via BLAST search) or through matches to domain databases such as CDD [18], PFAM [9], CATH [10], and FIGFAMs [19].…”

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confidence: 99%