scholarly journals Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases

1996 ◽  
Vol 5 (6) ◽  
pp. 1067-1080 ◽  
Author(s):  
John Kuszewski ◽  
Angela M. Gronenborn ◽  
G. Marius Clore
Keyword(s):  
Protein Structures ◽  
Structure Databases

scholarly journals Macromolecular Structure Databases: Past Progress and Future Challenges

1998 ◽  
Vol 54 (6) ◽  
pp. 1085-1094 ◽  
Author(s):  
Helge Weissig ◽  
Ilya N. Shindyalov ◽  
Philip E. Bourne
Keyword(s):  
Management Practices ◽  
Temporal Trends ◽  
Protein Structures ◽  
Data Bank ◽  
Macromolecular Structure ◽  
Paper Briefly ◽  
Future Challenges ◽  
Structure Databases ◽  
Full Discussion ◽  
Self Consistency

Databases containing macromolecular structure data provide a crystallographer with important tools for use in solving, refining and understanding the functional significance of their protein structures. Given this importance, this paper briefly summarizes past progress by outlining the features of the significant number of relevant databases developed to date. One recent database, PDB+, containing all current and obsolete structures deposited with the Protein Data Bank (PDB) is discussed in more detail. PDB+ has been used to analyze the self-consistency of the current (1 January 1998) corpus of over 7000 structures. A summary of those findings is presented (a full discussion will appear elsewhere) in the form of global and temporal trends within the data. These trends indicate that challenges exist if crystallographers are to provide the community with complete and consistent structural results in the future. It is argued that better information management practices are required to meet these challenges.

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

2013 ◽  
Vol 184 (12) ◽  
pp. 2860-2865 ◽  
Author(s):  
E. Sarti ◽  
S. Zamuner ◽  
P. Cossio ◽  
A. Laio ◽  
F. Seno ◽  
...  
Keyword(s):  
Protein Structures ◽  
Large Sets

Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

2014 ◽  
Vol 70 (7) ◽  
pp. 1994-2006 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Giuliana Comunale ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Experimental Information ◽  
Atomic Resolution ◽  
Data Sets ◽  
Density Maps ◽  
Combined Use ◽  
Final Electron ◽  
Automatic Model Building

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.

Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures

2012 ◽  
Vol 53 (3) ◽  
pp. 167-180 ◽  
Author(s):  
Mark Berjanskii ◽  
Jianjun Zhou ◽  
Yongjie Liang ◽  
Guohui Lin ◽  
David S. Wishart
Keyword(s):  
Protein Structures ◽  
Simple Measure

scholarly journals Computational investigation of marine bioactive compounds reveals frigocyclinone as a potent inhibitor of Kaposi’s Sarcoma Associated Herpesvirus (KSHV) targets

2019 ◽  
Vol 12 (3) ◽  
pp. 1289-1302
Author(s):  
Nirmaladevi Ponnusamy ◽  
Rajasree Odumpatta ◽  
Pavithra Damodharan ◽  
Mohanapriya Arumugam
Keyword(s):  
Bioactive Compounds ◽  
Drug Targets ◽  
Kaposi's Sarcoma ◽  
Protein Structures ◽  
In Silico Analysis ◽  
Kaposi’S Sarcoma ◽  
The Stability ◽  
Salicylihalamide A ◽  
Experimental Structure

In the present study, in silico analysis was employed to identify the action of marine bioactive compounds against KSHV targets. Virulence factor analysis of KSHV from literature review, three proteins LANA1, vIRF3/LANA2 and PF-8 were identified as putative drug targets. The quality of protein structures play a significant role in the experimental structure validation and prediction, where the predicted structures may contain considerable errors was checked by SAVES v5.0 servers. By virtual screening four potential bioactive compounds Ascorbic acid, Salicylihalamide A, Salicylihalamide B and Frigocyclinone were predicted. One of the potential compounds of Frigocyclinone has acting against KSHV proteins. Hence, determined as the good lead molecule against KSHV. Molecular dynamic simulation studies revealed the stability of LANA1- Frigocyclinone complex and it could be a futuristic perspective chemical compound for Kaposi’s sarcoma.

scholarly journals THE STUDY OF QUALITY INDICATORS AND FRACTIONAL COMPOSITION OF WHEAT GRAIN PROTEIN OF SOUTHERN REGIONS OF UKRAINE

2021 ◽  
Vol 20 (4) ◽  
pp. 4-10
Author(s):  
A. Penaki ◽  
A. Borta
Keyword(s):  
Moisture Content ◽  
Protein Content ◽  
Bulk Density ◽  
Quality Indicators ◽  
Protein Structures ◽  
Protein Fractions ◽  
Falling Number ◽  
Wheat Grain ◽  
Molecular Weights

The results of studies of the quality of food and non-food grain of wheat from the southern regions of Ukraine in 2016 harvest are presented. The indicators of the quality of wheat grain were determined, the uniformity of their distribution in different classes of wheat was assessed, the content of protein fractions of the gluten complex and the molecular weights of individual protein structures were determined. It was found that the studied 13 samples of wheat grain had the following quality indicators: moisture content 9.4 ... 13.5%, bulk density 731 ... 814 g/l, protein content 10.1 ... 13.2%, gluten content 16.4 ... 25.6%, gluten quality 50 ... 110 units of the IDK device, falling number 311 ... 493 s, grain admixture 1.2 ... 10.5%, grains damaged by a wheat bug, 0.1 ... 10.1%. It was noted that the bulk density of all samples of wheat of 2 ... 6 classes exceeded the standard values in each class. In terms of protein content, 2 from 3 samples of class 5 wheat and 1 from 2 samples of 6 class exceeded the standard value of class 3 wheat (≥11.0%). The same was observed for these samples and for the gluten content (≥18%). Almost all grain samples, except for 2 samples of the 5th class and 2 samples of the 6th class, met the requirements of wheat of the 2nd class (45 ... 100 units device VDK). The falling number of all samples was high and significantly exceeded the normalized value (180 s), even for class 2 wheat. It was found that the uniformity of the distribution of individual quality indicators in different classes of wheat grain by the coefficient of variation is not the same. Such indicators of grain quality as moisture content, bulk density and protein content in different samples of the south of Ukraine in 2016 harvest fluctuated weakly (V≤10%), in terms of the amount of gluten and the falling number fluctuations were average (10% ≤V≤20%). Fluctuations in the content of grain impurities and grains damaged by the wheat bug are big (V≥20%). For the last indicator, fluctuations relative to the average are very large and exceed 120 %. This indicates that in different areas where wheat was grown, the infestation by the wheat bug was very different. It was shown that regardless of the total amount of protein determined by the Infratec FOSS express analyzer, four protein fractions of the gluten complex (albumins, globulins, gliadins and glutenins) are present in all grain classes, and the molecular weights of the protein structures of the main fractions are within small limits, which are in kDa - for albumins and globulins 20...30, gliadins 27.. 100 and glutenins 30...35. It was noted that in the varietal wheat "Chernobrova" albumins and globulins have a slightly higher molecular weight (30...40 kDa) than in non-varietal wheat.

scholarly journals Controllable phycobilin modification: an alternative photoacclimation response in cryptophyte algae

2021 ◽  
Author(s):  
Leah Spangler ◽  
Mina Yu ◽  
Philip Jeffrey ◽  
Gregory Scholes
Keyword(s):  
Light Harvesting ◽  
Protein Structures ◽  
Green Light ◽  
Beta Subunits ◽  
Light Conditions ◽  
Low Light ◽  
Pump Probe ◽  
Light Harvesting Complex ◽  
Probe Spectroscopy

Cryptophyte algae are well known for their ability to survive under low light conditions through the use of their auxiliary light harvesting antennas, phycobiliproteins. Mainly acting to absorb light where chlorophyll cannot (500-650 nm), phycobiliproteins also play an instrumental role in helping cryptophyte algae respond to changes in light intensity through the process of photoacclimation. Until recently, photoacclimation in cryptophyte algae was only observed as a change in the cellular concentration of phycobiliproteins; however, an additional photoacclimation response was recently discovered that causes shifts in the phycobiliprotein absorbance peaks following growth under red, blue, or green light. Here, we reproduce this newly identified photoacclimation response in two other species of cryptophyte algae, P. sulcata and H. pacifica, and elucidate the origin of the response on the protein level. We compare isolated native and photoacclimated phycobiliproteins for these two species using spectroscopy and mass spectrometry, and we report the x-ray structures of the PC577 light harvesting complex and corresponding photoacclimated complex. We find that neither the protein sequences, nor the protein structures are modified by photoacclimation. We conclude that cryptophyte algae change a chromophore in one site of their phycobiliprotein beta-subunits as part of the photoacclimation response to changes in the spectral quality of light. Ultrafast pump-probe spectroscopy shows that the energy transfer is weakly affected by the photoacclimation.

scholarly journals Analytical tools in protein structure determination

2021 ◽  
Vol 8 (3) ◽  
pp. 103-111
Author(s):  
Krishna R Gupta ◽  
Uttam Patle ◽  
Uma Kabra ◽  
P. Mishra ◽  
Milind J Umekar
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Computational Techniques ◽  
Determination Process ◽  
Structure Databases ◽  
Analytical Tools

Three-dimensional protein structure prediction from amino acid sequence has been a thought-provoking task for decades, but it of pivotal importance as it provides a better understanding of its function. In recent years, the methods for prediction of protein structures have advanced considerably. Computational techniques and increase in protein sequence and structure databases have influence the laborious protein structure determination process. Still there is no single method which can predict all the protein structures. In this review, we describe the four stages of protein structure determination. We have also explored the currenttechniques used to uncover the protein structure and highpoint best suitable method for a given protein.

scholarly journals Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 549
Author(s):  
Romain Amyot ◽  
Yuichi Togashi ◽  
Holger Flechsig
Keyword(s):  
Conformational Dynamics ◽  
Protein Structures ◽  
Network Models ◽  
Chemical Information ◽  
Sequence Information ◽  
Large Set ◽  
Elastic Networks ◽  
Model Variant ◽  
Anisotropic Network

Simple protein elastic networks which neglect amino-acid information often yield reasonable predictions of conformational dynamics and are broadly used. Recently, model variants which incorporate sequence-specific and distance-dependent interactions of residue pairs have been constructed and demonstrated to improve agreement with experimental data. We have applied the new variants in a systematic study of protein fluctuation properties and compared their predictions with those of conventional anisotropic network models. We find that the quality of predictions is frequently linked to poor estimations in highly flexible protein regions. An analysis of a large set of protein structures shows that fluctuations of very weakly connected network residues are intrinsically prone to be significantly overestimated by all models. This problem persists in the new models and is not resolved by taking into account sequence information. The effect becomes even enhanced in the model variant which takes into account very soft long-ranged residue interactions. Beyond these shortcomings, we find that model predictions are largely insensitive to the integration of chemical information, at least regarding the fluctuation properties of individual residues. One can furthermore conclude that the inherent drawbacks may present a serious hindrance when improvement of elastic network models are attempted.

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