scholarly journals Determining protein structures using genetics

2018 ◽  
Author(s):  
Jörn M. Schmiedel ◽  
Ben Lehner
Keyword(s):  
Structure Determination ◽  
Low Cost ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biological Research ◽  
X Ray Crystallography ◽  
Close Relationship ◽  
And Function

SummaryDetermining the three dimensional structures of macromolecules is a major goal of biological research because of the close relationship between structure and function. Structure determination usually relies on physical techniques including x-ray crystallography, NMR spectroscopy and cryo-electron microscopy. Here we present a method that allows the high-resolution three-dimensional structure of a biological macromolecule to be determined only from measurements of the activity of mutant variants of the molecule. This genetic approach to structure determination relies on the quantification of genetic interactions (epistasis) between mutations and the discrimination of direct from indirect interactions. This provides a new experimental strategy for structure determination, with the potential to reveal functional and in vivo structural conformations at low cost and high throughput.

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

2019 ◽  
Vol 52 (6) ◽  
pp. 1422-1426
Author(s):  
Rajendran Santhosh ◽  
Namrata Bankoti ◽  
Adgonda Malgonnavar Padmashri ◽  
Daliah Michael ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Data Bank ◽  
Protein Crystal ◽  
Dimensional Structure ◽  
Protein Structure Analysis ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Polypeptide Chains

Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Recent Advances in Aptasensor for Cytokine Detection: A Review

Sensors ◽  
2021 ◽  
Vol 21 (24) ◽  
pp. 8491
Author(s):  
Jinmyeong Kim ◽  
Seungwoo Noh ◽  
Jeong Ah Park ◽  
Sang-Chan Park ◽  
Seong Jun Park ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Physiological Role ◽  
Dimensional Structure ◽  
Biological Research ◽  
Immune Modulators ◽  
Production Methods ◽  
Cytokine Detection ◽  
Cell Signal Transduction ◽  
Excessive Secretion

Cytokines are proteins secreted by immune cells. They promote cell signal transduction and are involved in cell replication, death, and recovery. Cytokines are immune modulators, but their excessive secretion causes uncontrolled inflammation that attacks normal cells. Considering the properties of cytokines, monitoring the secretion of cytokines in vivo is of great value for medical and biological research. In this review, we offer a report on recent studies for cytokine detection, especially studies on aptasensors using aptamers. Aptamers are single strand nucleic acids that form a stable three-dimensional structure and have been receiving attention due to various characteristics such as simple production methods, low molecular weight, and ease of modification while performing a physiological role similar to antibodies.

scholarly journals Structure and function of one unclassified-class glutathione S-transferase in Leptinotarsa decemlineata

2021 ◽  
Author(s):  
Yanjun Liu ◽  
Timothy W Moural ◽  
Sonu BK Koirala ◽  
Jonathan Hernandez ◽  
Zhongjian Shen ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Three Dimensional ◽  
Large Family ◽  
Dimensional Structure ◽  
Glutathione S Transferase ◽  
X Ray Crystallography ◽  
Xenobiotic Exposure ◽  
Multifunctional Enzymes ◽  
Glutathione S Transferases ◽  
And Function

Arthropod Glutathione S-transferases (GSTs) constitute a large family of multifunctional enzymes that are mainly associated with xenobiotic or stress adaptation. GST-mediated xenobiotic adaptation is through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. To date, the roles of GSTs in xenobiotic adaptation in the Colorado potato beetle (CPB), a notorious agriculture pest of plants within Solanaceae have not been well studied. Here, we functionally expressed and characterized an unclassified-class GST, LdGSTu1. The three-dimensional structure of the LdGSTu1 was solved with a resolution up to 1.8 Å by x-ray crystallography. Recombinant LdGSTu1 was used to determine enzyme activity and kinetic parameters using 1-chloro-2,4-dinitrobenzene (CDNB), GSH, p-nitrophenyl acetate (PNA) as substrates. The enzyme kinetic parameters and enzyme-substrate interaction studies demonstrated that LdGSTu1 could catalyze the conjugation of GSH to both CDNB and PNA, with a higher turnover number for CDNB than PNA. The LdGSTu1 enzyme inhibition assays demonstrated that the enzymatic conjugation of GSH to CDNB could be inhibited by multiple pesticides, suggesting a potential function of LdGSTu1 in xenobiotic adaptation.

Enhancing the Three-Dimensional Structure of Adherent Gingival Fibroblasts and Spheroids via a Fibrous Protein-Based Hydrogel Cover

2016 ◽  
Vol 202 (5-6) ◽  
pp. 343-354 ◽  
Author(s):  
Gili Kaufman ◽  
Laiz Nunes ◽  
Alex Eftimiades ◽  
Wojtek Tutak
Keyword(s):  
Three Dimensional ◽  
Building Blocks ◽  
Dimensional Structure ◽  
Sox2 Expression ◽  
Tissue Culture Polystyrene ◽  
Fibrous Protein ◽  
Confocal Scanning ◽  
Fibroblast Spheroids ◽  
And Function

Tissue engineering-based therapies rely on the delivery of monolayered fibroblasts on two-dimensional polystyrene-coated and extracellular matrix (ECM) surfaces to regenerate connective tissues. However, this approach may fail to mimic their three-dimensional (3D) native architecture and function. We hypothesize that ECM fibrous proteins, which direct the migration of cells in vivo, may attach and guide polystyrene- and Matrigel™-ECM (M-ECM)-adherent fibroblasts to rearrangement into large multicellular macrostructures with the ability to proliferate. Gingival monolayered fibroblasts and their derived spheroids were added and adhered to tissue culture polystyrene and M-ECM surfaces. The cells were covered with a layer of collagen1 hydrogel combined with vitronectin, fibronectin or fibrin, or 10% M-ECM. The development of 3D cell constructs was characterized by epifluorescence and confocal scanning microscope image analysis. The ECM turnover and the proliferative capabilities of the fibroblasts were determined via gene expression profiling of collagen1, fibronectin, matrix metalloproteinase/metallopeptidase 2, Nanog, and SRY (sex-determining region Y)-box2 (Sox2). Expression of the Sox2 protein was followed by immunostaining. The collagen1 protein had the strongest effect on monolayered and spheroid cell rearrangements, forming large spherical shapes and fused 3D macroconstructs. The addition of fibrin protein was typically required to achieve a similar effect on M-ECM-adherent monolayered fibroblasts. The spheroid fusion process was followed by an increase in cell density and the formation of tight clusters. The fused spheroids continued to maintain their intracellular ECM turnover and proliferation capacities. Collagen1 is a valuable component in the rearrangement of adherent fibroblast monolayers and spheroids. Fibroblast spheroids should preferably be used as basic building blocks to assemble multicellular connective tissue-like macrostructures.

scholarly journals PROBABILISTIC ENSEMBLES FOR IMPROVED INFERENCE IN PROTEIN-STRUCTURE DETERMINATION

2012 ◽  
Vol 10 (01) ◽  
pp. 1240009 ◽  
Author(s):  
AMEET SONI ◽  
JUDE SHAVLIK
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Complex Problem ◽  
Approximate Inference ◽  
X Ray ◽  
X Ray Crystallography ◽  
Inference Methods

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. While previous results have shown ACMI to be the state-of-the-art method on this task, its approximate inference algorithm remains computationally expensive and susceptible to errors. In this work, we develop Probabilistic Ensembles in ACMI (PEA), a framework for leveraging multiple, independent runs of approximate inference to produce estimates of protein structures. Our results show statistically significant improvements in the accuracy of inference resulting in more complete and accurate protein structures. In addition, PEA provides a general framework for advanced approximate inference methods in complex problem domains.

Mutational studies of protein structures and their stabilities

1992 ◽  
Vol 25 (2) ◽  
pp. 205-250 ◽  
Author(s):  
David Shortle
Keyword(s):  
Amino Acid ◽  
Functional Role ◽  
Hydrophobic Interactions ◽  
Protein Structures ◽  
Three Dimensional ◽  
Rnase A ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
X Ray Crystallography ◽  
And Function

The fundamental relationship between structure and function has served to guide investigations into the workings of living systems at all levels - from the whole organism to individual cells on down to individual molecules. When X-ray crystallography began to reveal the three-dimensional structures of proteins like myoglobin, lysozyme and RNase A, protein chemists were well prepared to draw inferences about functional mechanisms from the precise positioning of amino acid residues they could see. The close proximity between an amino acid side chain and a chemical group on a bound ligand strongly suggests a functional role for that side chain in binding affinity and specificity. Likewise, the nearly universal finding of large clusters of hydrophobic side chains buried in the core of proteins strongly supports a major functional role of hydrophobic interactions in protein folding and stability. Even though eminently plausible hypotheses like these, grounded in the most fundamental principles of chemistry and the logic of structure–function relationships, become widely accepted and make their way into textbooks, protein chemists have felt compelled to search for ways to test them and put them on a more quantitative basis.

scholarly journals A COMPARATIVE STUDY OF PROTEIN TERTIARY STRUCTURE PREDICTION METHODS

2014 ◽  
pp. 15-18
Author(s):  
CHANDRAYANI N. ROKDE ◽  
DR.MANALI KSHIRSAGAR
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Sequence Data ◽  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Dimensional Structure ◽  
X Ray Crystallography ◽  
Protein Tertiary Structure Prediction

Protein structure prediction (PSP) from amino acid sequence is one of the high focus problems in bioinformatics today. This is due to the fact that the biological function of the protein is determined by its three dimensional structure. The understanding of protein structures is vital to determine the function of a protein and its interaction with DNA, RNA and enzyme. Thus, protein structure is a fundamental area of computational biology. Its importance is intensed by large amounts of sequence data coming from PDB (Protein Data Bank) and the fact that experimentally methods such as X-ray crystallography or Nuclear Magnetic Resonance (NMR)which are used to determining protein structures remains very expensive and time consuming. In this paper, different types of protein structures and methods for its prediction are described.

scholarly journals Improving diffraction resolution using a new dehydration method

2016 ◽  
Vol 72 (2) ◽  
pp. 152-159 ◽  
Author(s):  
Qingqiu Huang ◽  
Doletha M. E. Szebenyi
Keyword(s):  
Escherichia Coli ◽  
Structure Determination ◽  
Three Dimensional ◽  
Archaeoglobus Fulgidus ◽  
Dimensional Structure ◽  
High Quality ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Dry Out

The production of high-quality crystals is one of the major obstacles in determining the three-dimensional structure of macromolecules by X-ray crystallography. It is fairly common that a visually well formed crystal diffracts poorly to a resolution that is too low to be suitable for structure determination. Dehydration has proven to be an effective post-crystallization treatment for improving crystal diffraction quality. Several dehydration methods have been developed, but no single one of them is suitable for all crystals. Here, a new convenient and effective dehydration method is reported that makes use of a dehydrating solution that will not dry out in air for several hours. Using this dehydration method, the resolution ofArchaeoglobus fulgidusCas5a crystals has been increased from 3.2 to 1.95 Å and the resolution ofEscherichia coliLptA crystals has been increased from <5 to 3.4 Å.

scholarly journals Purification, characterization and function of bacterioferritin from the cyanobacterium Synechocystis P.C.C. 6803

1992 ◽  
Vol 281 (3) ◽  
pp. 785-793 ◽  
Author(s):  
J P Laulhère ◽  
A M Labouré ◽  
O Van Wuytswinkel ◽  
J Gagnon ◽  
J F Briat
Keyword(s):  
Molecular Mass ◽  
Sequence Similarity ◽  
Iron Status ◽  
Iron Concentration ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Cellular Iron ◽  
And Function

Storage and buffering of iron is achieved by a class of proteins, the ferritins, widely distributed throughout the living kingdoms. All ferritins have in common their three-dimensional structure and their ability to store large amounts of iron in their central cavity. However, eukaryotic ferritins from plants and animals and bacterioferritins have no sequence similarity, and besides non-haem iron bacterioferritins contain haem residues whereas eukaryotic ferritins do not. In this paper we report the first purification and characterization of a bacterioferritin from a cyanobacterium. It has a molecular mass of 400 kDa and is built up from 19 kDa subunits. Its N-terminal sequence shows 73% identity with that of the Escherichia coli bacterioferritin subunit. It contains 2300 atoms of iron and 1500 molecules of phosphate per ferritin molecule and 0.25 haem residue per subunit; the alpha-peak of the cytochrome has its maximum at 559 nm. In contrast with what is known for eukaryotic ferritins, we found that bacterioferritin from Synechocystis is not inducible by iron under the conditions that we have tested and that it has a constant concentration whatever the iron status of the cells, even at very low iron concentration. Bacterioferritin from Synechocystis P.C.C. 6803 is fully assembled in vivo and it is shown by labelling with 59Fe that it is able to load iron in vitro as well as in vivo. Bacterioferritin from Synechocystis is shown to have an iron-buffering function while the bulk of cellular iron is found associated with a pool of low-molecular-mass electronegative molecules. The role of Synechocystis bacterioferritin in iron metabolism is discussed.

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