scholarly journals Family permutation profiling identifies a dynamic protein domain as functionally tolerant to increased conformational entropy

2019 ◽  
Author(s):  
Joshua T. Atkinson ◽  
Alicia M. Jones ◽  
Vikas Nanda ◽  
Jonathan J. Silberg
Keyword(s):  
Enzymatic Activity ◽  
Melting Temperature ◽  
Primary Structure ◽  
Adenylate Kinase ◽  
Protein Domain ◽  
Conformational Entropy ◽  
Peptide Bonds ◽  
Positional Tolerance ◽  
And Function ◽  
New Protein

ABSTRACTTo investigate whether adenylate kinase (AK) homologs differ in their functional tolerance to mutational lesions that alter dynamics, we subjected three homologs having a range of thermostabilities to random circular permutation and evaluated where new protein termini were non-disruptive to activity using a cellular selection and deep mutational scanning. Analysis of the positional tolerance to new termini, which increase local conformational entropy by breaking peptide bonds, showed that bonds were either functionally sensitive to cleavage across all three homologs, differentially sensitive, or uniformly tolerant. The mobile AMP binding domain, which displays the highest calculated contact energies (frustration), presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. Thus, regions of high energetic frustration tolerated increases in conformational entropy in a manner that was less dependent on thermostability than regions of lower frustration. Our results suggest that family permutation profiling identifies primary structure that has been selected by evolution for high frustration that is critical to enzymatic activity. They also illustrate how deep mutational scanning can be applied to protein homologs in parallel to learn how topology and function govern mutational tolerance.

scholarly journals Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts

2019 ◽  
Vol 32 (11) ◽  
pp. 489-501
Author(s):  
Joshua T Atkinson ◽  
Alicia M Jones ◽  
Vikas Nanda ◽  
Jonathan J Silberg
Keyword(s):  
Melting Temperature ◽  
Primary Structure ◽  
Adenylate Kinase ◽  
Conformational Flexibility ◽  
Circular Permutation ◽  
Binding Domain ◽  
Enzyme Family ◽  
Residue Contacts ◽  
Positional Tolerance ◽  
New Protein

Abstract Adenylate kinase (AK) orthologs with a range of thermostabilities were subjected to random circular permutation, and deep mutational scanning was used to evaluate where new protein termini were nondisruptive to activity. The fraction of circularly permuted variants that retained function in each library correlated with AK thermostability. In addition, analysis of the positional tolerance to new termini, which increase local conformational flexibility, showed that bonds were either functionally sensitive to cleavage across all homologs, differentially sensitive, or uniformly tolerant. The mobile AMP-binding domain, which displays the highest calculated contact energies, presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. These results show that family permutation profiling identifies primary structure that has been selected by evolution for dynamics that are critical to activity within an enzyme family. These findings also illustrate how deep mutational scanning can be applied to protein homologs in parallel to differentiate how topology, stability, and local energetics govern mutational tolerance.

scholarly journals Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function

2017 ◽  
Vol 91 (23) ◽  
Author(s):  
Wenhua Kuang ◽  
Huanyu Zhang ◽  
Manli Wang ◽  
Ning-Yi Zhou ◽  
Fei Deng ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Active Site ◽  
Salt Bridge ◽  
Sulfhydryl Oxidase ◽  
Dimer Interface ◽  
Conserved Regions ◽  
Occlusion Bodies ◽  
Budded Virus ◽  
And Function ◽  
Substrate Proteins

ABSTRACT Baculoviruses encode a conserved sulfhydryl oxidase, P33, which is necessary for budded virus (BV) production and multinucleocapsid occlusion-derived virus (ODV) formation. Here, the structural and functional relationship of P33 was revealed by X-ray crystallography, site-directed mutagenesis, and functional analysis. Based on crystallographic characterization and structural analysis, a series of P33 mutants within three conserved regions, i.e., the active site, the dimer interface, and the R127-E183 salt bridge, were constructed. In vitro experiments showed that mutations within the active site and dimer interface severely impaired the sulfhydryl oxidase activity of P33, while the mutations in the salt bridge had a relatively minor influence. Recombinant viruses containing mutated P33 were constructed and assayed in vivo. Except for the active-site mutant AXXA, all other mutants produced infectious BVs, although certain mutants had a decreased BV production. The active-site mutant H114A, the dimer interface mutant H227D, and the salt bridge mutant R127A-E183A were further analyzed by electron microscopy and bioassays. The occlusion bodies (OBs) of mutants H114A and R127A-E183A had a ragged surface and contained mostly ODVs with a single nucleocapsid. The OBs of all three mutants contained lower numbers of ODVs and had a significantly reduced oral infectivity in comparison to control virus. Crystallographic analyses further revealed that all three regions may coordinate with one another to achieve optimal function of P33. Taken together, our data revealed that all the three conserved regions are involved in P33 activity and are crucial for virus morphogenesis and peroral infectivity. IMPORTANCE Sulfhydryl oxidase catalyzes disulfide bond formation of substrate proteins. P33, a baculovirus-encoded sulfhydryl oxidase, is different from other cellular and viral sulfhydryl oxidases, bearing unique features in tertiary and quaternary structure organizations. In this study, we found that three conserved regions, i.e., the active site, dimer interface, and the R127-E183 salt bridge, play important roles in the enzymatic activity and function of P33. Previous observations showed that deletion of p33 results in a total loss of budded virus (BV) production and in morphological changes in occlusion-derived virus (ODV). Our study revealed that certain P33 mutants lead to occlusion bodies (OBs) with a ragged surface, decreased embedded ODVs, and reduced oral infectivity. Interestingly, some P33 mutants with impaired ODV/OB still retained BV productivity, indicating that the impacts on BV and on ODV/OB are two distinctly different functions of P33, which are likely to be performed via different substrate proteins.

scholarly journals The encapsulin from Thermatoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein

2021 ◽  
Author(s):  
Benjamin J LaFrance ◽  
Caleb Cassidy-Amstutz ◽  
Robert J Nichols ◽  
Luke M Oltrogge ◽  
Eva Nogales ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Biochemical Analysis ◽  
Active Role ◽  
Structure And Function ◽  
Redox Active ◽  
Cargo Protein ◽  
Cargo Proteins ◽  
And Function ◽  
Flavin Binding ◽  
Unique Chemical

Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based "organelles" found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~25-50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure-function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model T. maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryoEM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the T. maritima encapsulin, the decameric cargo protein with 5-fold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier-it also plays a significant role in the structure and function of the cargo enzyme.

scholarly journals Function Prediction from Protein Primary Structure using Deep Learning LSTM Algorithm

2019 ◽  
Vol 8 (4) ◽  
pp. 4355-4359
Keyword(s):  
Nervous System ◽  
Prion Protein ◽  
Primary Structure ◽  
Protein Function ◽  
Function Prediction ◽  
Biological Information ◽  
Essential Information ◽  
Diverse Field ◽  
Protein Primary Structure ◽  
And Function

Biological information of protein primary structure is responsible for finding the protein function, extracting features and function of a protein in the biology lab is challenging and time-consuming. Identification of protein function provides essential information for the treatment of various diseases and drug design. Therefore, extracting the protein knowledge from primary structure alone has been a diverse field in the study of bioinformatics data mining and computational biology. This study aimed to function prediction of protein primary structure using the LSTM methods. PRNP(prion protein )most of the nervous system tissues express by prion protein, this is generally to protease-resistant from disease, due to this reasons, the human codon PRNP is most closely associated with Alzheimer disease. The PRNP protein data trained with Hemo sapiens PRNP selection, classification was implemented with network layer perceptron. The learning algorithms are frame by the nervous system. The training results observation indicate that the learning success of prion protein classification leads positively.

scholarly journals LAMP2: a major update of the database linking antimicrobial peptides

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Guizi Ye ◽  
Hongyu Wu ◽  
Jinjiang Huang ◽  
Wei Wang ◽  
Kuikui Ge ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Primary Structure ◽  
Scientific Community ◽  
Resistant Bacteria ◽  
Drug Resistant ◽  
Current Version ◽  
Functional Activities ◽  
Drug Resistant Bacteria ◽  
Functional Classes ◽  
And Function

Abstract Antimicrobial peptides (AMPs) have been regarded as a potential weapon to fight against drug-resistant bacteria, which is threating the globe. Thus, more and more AMPs had been designed or identified. There is a need to integrate them into a platform for researchers to facilitate investigation and analyze existing AMPs. The AMP database has become an important tool for the discovery and transformation of AMPs as agents. A database linking antimicrobial peptides (LAMPs), launched in 2013, serves as a comprehensive tool to supply exhaustive information of AMP on a single platform. LAMP2, an updated version of LAMP, holds 23 253 unique AMP sequences and expands to link 16 public AMP databases. In the current version, there are more than 50% (12 236) sequences only linking a single database and more than 45% of AMPs linking two or more database links. Additionally, updated categories based on primary structure, collection, composition, source and function have been integrated into LAMP2. Peptides in LAMP2 have been integrated in 8 major functional classes and 38 functional activities. More than 89% (20 909) of the peptides are experimentally validated peptides. A total of 1924 references were extracted and regarded as the evidence for supporting AMP activity and cytotoxicity. The updated version will be helpful to the scientific community.

Subunit δ of Chloroplast F0F1 ATPase and OSCP of Mitochondrial F0F1 ATPase: a Comparison by CD-Spectroscopy

1991 ◽  
Vol 46 (9-10) ◽  
pp. 759-764 ◽  
Author(s):  
Siegfried Engelbrecht ◽  
Jennifer Reed ◽  
François Penin ◽  
Danièle C. Gautheron ◽  
Wolfgang Junge
Keyword(s):  
Primary Structure ◽  
Tertiary Structure ◽  
Atp Synthesis ◽  
Structural Similarity ◽  
Cd Spectroscopy ◽  
Α Helix ◽  
And Function ◽  
High Degree ◽  
Very High ◽  
Secondary And Tertiary Structure

Abstract CD spectra have been recorded with subunit δ from chloroplast CF0CF1 and with OSCP from mitochondrial MF0MF1. These subunits are supposed to act similarly at the interface between proton transport through the F0-portion and ATP-synthesis in the F1-portion of their respective F0F1-ATPase. Evaluation of the data for both proteins revealed a very high α-helix content of -85% and practically no β-sheets. Despite their low homology on the primary structure level (23% identity) and their different electrostatic properties (pl-values differ by 3 units), spinach δ and porcine OSCP are indistinguishable with respect to their secondary structure as measured by CD. Prediction and analysis of consensual a-helices even in poorly conserved regions indicate α high degree of structural similarity between chloroplast δ and OSCP. In view of the topology and function of δ and OSCP in intact F0F1 these findings are interpreted to indicate the dominance of secondary and tertiary structure over the primary structure in their supposed function between proton flow and ATP-synthesis.

Protein Domain and Function Prediction Resources

2013 ◽  
pp. 1773-1775
Author(s):  
Annette A. Alcasabas
Keyword(s):  
Function Prediction ◽  
Protein Domain ◽  
And Function

scholarly journals SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction

2001 ◽  
Vol 2 (4) ◽  
pp. 226-235 ◽  
Author(s):  
Amanda Cottage ◽  
Yvonne J. K. Edwards ◽  
Greg Elgar
Keyword(s):  
Genomic Sequence ◽  
Protein Family ◽  
Sequence Motifs ◽  
Est Database ◽  
Computational Tools ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs ◽  
And Function ◽  
New Protein ◽  
Genomic Organisation

As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence fromFugu rubripes, we identified a novel gene,SAND, with significant sequence identity to hypothetical proteins predicted inSaccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, aDrosophila melanogastergene, and mouse and human cDNAs. Here we identify a furtherSANDhomologue in human andArabidopsis thalianaby use of standard computational tools. We describe the genomic organisation ofSANDin these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.

Differential subcellular location and function of two isoenzymes of cardiac adenylate kinase

1981 ◽  
Vol 9 (6) ◽  
pp. 570-571
Author(s):  
ELAINE J. WALKER ◽  
JOCELYN W. DOW
Keyword(s):  
Adenylate Kinase ◽  
Subcellular Location ◽  
And Function

scholarly journals Inositol Pyrophosphate Pathways and Mechanisms: What Can We Learn from Plants?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2789 ◽  
Author(s):  
Caitlin Cridland ◽  
Glenda Gillaspy
Keyword(s):  
Inositol Phosphate ◽  
Specific Protein ◽  
Protein Domain ◽  
Growth And Survival ◽  
Inositol Pyrophosphate ◽  
Protein Partners ◽  
Inositol Pyrophosphates ◽  
Energy Sensing ◽  
And Function ◽  
Complex Signaling

The ability of an organism to maintain homeostasis in changing conditions is crucial for growth and survival. Eukaryotes have developed complex signaling pathways to adapt to a readily changing environment, including the inositol phosphate (InsP) signaling pathway. In plants and humans the pyrophosphorylated inositol molecules, inositol pyrophosphates (PP-InsPs), have been implicated in phosphate and energy sensing. PP-InsPs are synthesized from the phosphorylation of InsP6, the most abundant InsP. The plant PP-InsP synthesis pathway is similar but distinct from that of the human, which may reflect differences in how molecules such as Ins(1,4,5)P3 and InsP6 function in plants vs. animals. In addition, PP-InsPs can potentially interact with several major signaling proteins in plants, suggesting PP-InsPs play unique signaling roles via binding to protein partners. In this review, we will compare the biosynthesis and role of PP-InsPs in animals and plants, focusing on three central themes: InsP6 synthesis pathways, synthesis and regulation of the PP-InsPs, and function of a specific protein domain called the Syg1, Pho1, Xpr1 (SPX ) domain in binding PP-InsPs and regulating inorganic phosphate (Pi) sensing. This review will provide novel insights into the biosynthetic pathway and bioactivity of these key signaling molecules in plant and human systems.

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