scholarly journals A novel computational method for head-to-tail peptide cyclization: application to urotensin II

2022 ◽  
Author(s):  
Yasaman Karami ◽  
Samuel Murail ◽  
Julien Giribaldi ◽  
Benjamin Lefranc ◽  
Jerome Leprince ◽  
...  
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Protein Structures ◽  
Computational Method ◽  
Urotensin Ii ◽  
Peptide Cyclization ◽  
Linear Peptide ◽  
Structure Relationship ◽  
Head To Tail Cyclization

Peptides have recently re-gained interest as therapeutic candidates but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity and preventing enzymatic degradation. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to head-to-tail peptide cyclization. Firstly we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation improving by over 1 A over pre-existing protocols. Secondly, and more importantly, we show that is is possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational peptide head-to-tail cyclization. As functional validation, we apply it to the design of a head-to-tail cyclized derivative of urotensin II, an 11-residue long peptide which exerts a broad array of biologic activities, making its cognate receptor a valuable and innovative therapeutic or diagnostic target. We propose a three amino acid candidate linker, leading to the first synthesized 14-residue long cyclic UII analogue with excellent retention of in vitro activity.

Synthesis of Fragments of the Vasoactive Intestinal Peptide (VIP) and Analysis of Their Residual Biological Activities

1995 ◽  
Vol 60 (7) ◽  
pp. 1229-1235 ◽  
Author(s):  
Ivana Zoulíková ◽  
Ivan Svoboda ◽  
Jiří Velek ◽  
Václav Kašička ◽  
Jiřina Slaninová ◽  
...  
Keyword(s):  
Amino Acid ◽  
Biological Activities ◽  
Residual Activity ◽  
Detailed Examination ◽  
Amino Acid Residues ◽  
Linear Peptide ◽  
Zone Electrophoresis ◽  
Capillary Zone

The vasoactive intestinal (poly)peptide (VIP) is a linear peptide containing 28 amino acid residues, whose primary structure indicates a low metabolic stability. The following VIP fragments, as potential metabolites, and their analogues were prepared by synthesis on a solid: [His(Dnp)1]VIP(1-10), VIP(11-14), [D-Arg12]VIP(11-14), [Lys(Pac)15,21,Arg20]VIP(15-22), and VIP(23-28). After purification, the peptides were characterized by amino acid analysis, mass spectrometry, RP HPLC, and capillary zone electrophoresis. In some tests, detailed examination of the biological activity of the substances in vivo and in vitro gave evidence of a low, residual activity of some fragments, viz. a depressoric activity in vivo for [His(Dnp)1]VIP(1-10) and a stimulating activity for the release of α-amylase in vitro and in vivo for [Lys(Pac)15,21,Arg20]VIP(15-22) and VIP(23-28).

PROTEIN METAL BINDING RESIDUE PREDICTION BASED ON NEURAL NETWORKS

2005 ◽  
Vol 15 (01n02) ◽  
pp. 71-84 ◽  
Author(s):  
CHIN-TENG LIN ◽  
KEN-LI LIN ◽  
CHIH-HSIEN YANG ◽  
I-FANG CHUNG ◽  
CHUEN-DER HUANG ◽  
...  
Keyword(s):  
Neural Networks ◽  
Amino Acid ◽  
Metal Ions ◽  
Metal Binding ◽  
Protein Structures ◽  
Direct Analysis ◽  
Sequence Information ◽  
Amino Acid Residues ◽  
Binding Residue

Over one-third of protein structures contain metal ions, which are the necessary elements in life systems. Traditionally, structural biologists were used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpreting the function formation and reaction mechanism of enzyme by their structures and observations from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict the protein metal-binding amino acid residues from its sequence information only by neural networks with sliding window-based feature extraction and biological feature encoding techniques. In four major bulk elements (Calcium, Potassium, Magnesium, and Sodium), the metal-binding residues are identified by the proposed method with higher than 90% sensitivity and very good accuracy under 5-fold cross validation. With such promising results, it can be extended and used as a powerful methodology for metal-binding characterization from rapidly increasing protein sequences in the future.

scholarly journals PREMONITION - Preprocessing motifs in protein structures for search acceleration

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 217 ◽  
Author(s):  
Sandeep Chakraborty ◽  
Basuthkar J. Rao ◽  
Bjarni Asgeirsson ◽  
Ravindra Venkatramani ◽  
Abhaya M. Dandekar
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Active Site ◽  
Active Sites ◽  
Protein Structures ◽  
3D Structure ◽  
Search Space ◽  
Computational Method ◽  
Computational Time ◽  
Active Site Residues

The remarkable diversity in biological systems is rooted in the ability of the twenty naturally occurring amino acids to perform multifarious catalytic functions by creating unique structural scaffolds known as the active site. Finding such structrual motifs within the protein structure is a key aspect of many computational methods. The algorithm for obtaining combinations of motifs of a certain length, although polynomial in complexity, runs in non-trivial computer time. Also, the search space expands considerably if stereochemically equivalent residues are allowed to replace an amino acid in the motif. In the present work, we propose a method to precompile all possible motifs comprising of a set (n=4 in this case) of predefined amino acid residues from a protein structure that occur within a specified distance (R) of each other (PREMONITION). PREMONITION rolls a sphere of radius R along the protein fold centered at the C atom of each residue, and all possible motifs are extracted within this sphere. The number of residues that can occur within a sphere centered around a residue is bounded by physical constraints, thus setting an upper limit on the processing times. After such a pre-compilation step, the computational time required for querying a protein structure with multiple motifs is considerably reduced. Previously, we had proposed a computational method to estimate the promiscuity of proteins with known active site residues and 3D structure using a database of known active sites in proteins (CSA) by querying each protein with the active site motif of every other residue. The runtimes for such a comparison is reduced from days to hours using the PREMONITION methodology.

scholarly journals Targeting Human Thrombus by Liposomes Modified with Anti-Fibrin Protein Binders

Pharmaceutics ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 642 ◽  
Author(s):  
Hana Petroková ◽  
Josef Mašek ◽  
Milan Kuchař ◽  
Andrea Vítečková Wünschová ◽  
Jana Štikarová ◽  
...  
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Enzyme Linked Immunosorbent Assay ◽  
Ribosome Display ◽  
Amino Acid Peptide ◽  
His Tag ◽  
Insoluble Form ◽  
Protein Binders ◽  
Protein Variants

Development of tools for direct thrombus imaging represents a key step for diagnosis and treatment of stroke. Nanoliposomal carriers of contrast agents and thrombolytics can be functionalized to target blood thrombi by small protein binders with selectivity for fibrin domains uniquely formed on insoluble fibrin. We employed a highly complex combinatorial library derived from scaffold of 46 amino acid albumin-binding domain (ABD) of streptococcal protein G, and ribosome display, to identify variants recognizing fibrin cloth in human thrombus. We constructed a recombinant target as a stretch of three identical fibrin fragments of 16 amino acid peptide of the Bβ chain fused to TolA protein. Ribosome display selection followed by large-scale Enzyme-Linked ImmunoSorbent Assay (ELISA) screening provided four protein variants preferentially binding to insoluble form of human fibrin. The most specific binder variant D7 was further modified by C-terminal FLAG/His-Tag or double His-tag for the attachment onto the surface of nanoliposomes via metallochelating bond. D7-His-nanoliposomes were tested using in vitro flow model of coronary artery and their binding to fibrin fibers was demonstrated by confocal and electron microscopy. Thus, we present here the concept of fibrin-targeted binders as a platform for functionalization of nanoliposomes in the development of advanced imaging tools and future theranostics.

USING RIGIDITY ANALYSIS TO PROBE MUTATION-INDUCED STRUCTURAL CHANGES IN PROTEINS

2012 ◽  
Vol 10 (03) ◽  
pp. 1242010 ◽  
Author(s):  
FILIP JAGODZINSKI ◽  
JEANNE HARDY ◽  
ILEANA STREINU
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Structural Changes ◽  
Protein Structures ◽  
Data Bank ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Single Amino Acid ◽  
Fast Evaluation

Predicting the effect of a single amino acid substitution on the stability of a protein structure is a fundamental task in macromolecular modeling. It has relevance to drug design and understanding of disease-causing protein variants. We present KINARI-Mutagen, a web server for performing in silico mutation experiments on protein structures from the Protein Data Bank. Our rigidity-theoretical approach permits fast evaluation of the effects of mutations that may not be easy to perform in vitro, because it is not always possible to express a protein with a specific amino acid substitution. We use KINARI-Mutagen to identify critical residues, and we show that our predictions correlate with destabilizing mutations to glycine. In two in-depth case studies we show that the mutated residues identified by KINARI-Mutagen as critical correlate with experimental data, and would not have been identified by other methods such as Solvent Accessible Surface Area measurements or residue ranking by contributions to stabilizing interactions. We also generate 48 mutants for 14 proteins, and compare our rigidity-based results against experimental mutation stability data. KINARI-Mutagen is available at http://kinari.cs.umass.edu .

scholarly journals Flexibility and mobility of SARS-CoV-2-related protein structures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rudolf A. Römer ◽  
Navodya S. Römer ◽  
A. Katrine Wallis
Keyword(s):  
In Silico ◽  
Drug Targets ◽  
Large Scale ◽  
Structural Information ◽  
Protein Structures ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Related Protein

AbstractThe worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein—using its complete homo-trimer configuration with 2905 residues—our method identifies a large-scale opening and closing of the S1 subunit through movement of the S$${}^\text{B}$$ B domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.

scholarly journals Cellular labelling favours unfolded proteins

2018 ◽  
Author(s):  
David-Paul Minde ◽  
Manasa Ramakrishna ◽  
Kathryn S. Lilley
Keyword(s):  
Large Scale ◽  
Protein Structures ◽  
Unfolded Proteins ◽  
80S Ribosome ◽  
Unfolded Protein ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Wide Scale

AbstractFolded enzymes are essential for life, but there is limited in vivo information about how locally unfolded protein regions contribute to biological functions. Intrinsically Disordered Regions (IDRs) are enriched in disease-linked and multiply post-translationally modified proteins. The extent of foldability of predicted IDRs is difficult to measure due to significant technical challenges to survey in vivo protein conformations on a proteome-wide scale. We reasoned that IDRs should be more accessible to targeted in vivo biotinylation than more ordered protein regions, if they retain their flexibility in vivo. Indeed, we observed a positive correlation of predicted IDRs and biotinylation density across four independent large-scale proximity proteomics studies that together report >20 000 biotinylation sites. We show that biotin ‘painting’ is a promising approach to fill gaps in knowledge between static in vitro protein structures, in silico disorder predictions and in vivo condition-dependent subcellular plasticity using the 80S ribosome as an example.

scholarly journals Initial In Vitro and In Vivo Evaluation of a Novel CCK2R Targeting Peptide Analog Labeled with Lutetium-177

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4585
Author(s):  
Anton Amadeus Hörmann ◽  
Maximilian Klingler ◽  
Maliheh Rezaeianpour ◽  
Nikolas Hörmann ◽  
Ronald Gust ◽  
...  
Keyword(s):  
Amino Acid ◽  
Enzymatic Degradation ◽  
Cell Uptake ◽  
Receptor Interaction ◽  
In Vivo Evaluation ◽  
Linear Peptide ◽  
Peptide Analog ◽  
Targeting Peptide

Targeting of cholecystokinin-2 receptor (CCK2R) expressing tumors using radiolabeled minigastrin (MG) analogs is hampered by rapid digestion of the linear peptide in vivo. In this study, a new MG analog stabilized against enzymatic degradation was investigated in preclinical studies to characterize the metabolites formed in vivo. The new MG analog DOTA-DGlu-Pro-Tyr-Gly-Trp-(N-Me)Nle-Asp-1Nal-NH2 comprising site-specific amino acid substitutions in position 2, 6 and 8 and different possible metabolites thereof were synthesized. The receptor interaction of the peptide and selected metabolites was evaluated in a CCK2R-expressing cell line. The enzymatic stability of the 177Lu-labeled peptide analog was evaluated in vitro in different media as well as in BALB/c mice up to 1 h after injection and the metabolites were identified based on radio-HPLC analysis. The new radiopeptide showed a highly increased stability in vivo with >56% intact radiopeptide in the blood of BALB/c mice 1 h after injection. High CCK2R affinity and cell uptake was confirmed only for the intact peptide, whereas enzymatic cleavage within the receptor specific C-terminal amino acid sequence resulted in complete loss of affinity and cell uptake. A favorable biodistribution profile was observed in BALB/c mice with low background activity, preferential renal excretion and prolonged uptake in CCK2R-expressing tissues. The novel stabilized MG analog shows high potential for diagnostic and therapeutic use. The radiometabolites characterized give new insights into the enzymatic degradation in vivo.

scholarly journals Synchrony between daily rhythms of malaria parasites and hosts is driven by an essential amino acid

2021 ◽  
Vol 6 ◽  
pp. 186
Author(s):  
Kimberley F. Prior ◽  
Benita Middleton ◽  
Alíz T.Y. Owolabi ◽  
Mary L. Westwood ◽  
Jacob Holland ◽  
...  
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Time Of Day ◽  
Asexual Development ◽  
Host Feeding ◽  
Malaria Parasites ◽  
Disease Symptoms ◽  
Daily Rhythmicity

Background: Rapid asexual replication of blood stage malaria parasites is responsible for the severity of disease symptoms and fuels the production of transmission forms. Here, we demonstrate that the Plasmodium chabaudi’s schedule for asexual replication can be orchestrated by isoleucine, a metabolite provided to the parasite in periodic manner due to the host’s rhythmic intake of food. Methods: We infect female C57BL/6 and Per1/2-null TTFL clock-disrupted mice with 1×105 red blood cells containing P. chabaudi (DK genotype). We perturb the timing of rhythms in asexual replication and host feeding-fasting cycles to identify nutrients with rhythms that match all combinations of host and parasite rhythms. We then test whether perturbing the availability of the best candidate nutrient in vitro elicits changes their schedule for asexual development. Results: Our large-scale metabolomics experiment and follow up experiments reveal that only one metabolite - the amino acid isoleucine – fits criteria for a time-of-day cue used by parasites to set the schedule for replication. The response to isoleucine is a parasite strategy rather than solely the consequences of a constraint imposed by host rhythms, because unlike when parasites are deprived of other essential nutrients, they suffer no apparent costs from isoleucine withdrawal. Conclusions: Overall, our data suggest parasites can use the daily rhythmicity of blood-isoleucine concentration to synchronise asexual development with the availability of isoleucine, and potentially other resources, that arrive in the blood in a periodic manner due to the host’s daily feeding-fasting cycle. Identifying both how and why parasites keep time opens avenues for interventions; interfering with the parasite’s time-keeping mechanism may stall replication, increasing the efficacy of drugs and immune responses, and could also prevent parasites from entering dormancy to tolerate drugs.

scholarly journals Synchrony between daily rhythms of malaria parasites and hosts is driven by an essential amino acid

2021 ◽  
Vol 6 ◽  
pp. 186
Author(s):  
Kimberley F. Prior ◽  
Benita Middleton ◽  
Alíz T.Y. Owolabi ◽  
Mary L. Westwood ◽  
Jacob Holland ◽  
...  
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Time Of Day ◽  
Asexual Development ◽  
Host Feeding ◽  
Malaria Parasites ◽  
Disease Symptoms ◽  
Daily Rhythmicity

Background: Rapid asexual replication of blood stage malaria parasites is responsible for the severity of disease symptoms and fuels the production of transmission forms. Here, we demonstrate that a Plasmodium chabaudi’s schedule for asexual replication can be orchestrated by isoleucine, a metabolite provided to the parasite in a periodic manner due to the host’s rhythmic intake of food. Methods: We infect female C57BL/6 and Per1/2-null mice which have a disrupted canonical (transcription translation feedback loop, TTFL) clock with 1×105 red blood cells containing P. chabaudi (DK genotype). We perturb the timing of rhythms in asexual replication and host feeding-fasting cycles to identify nutrients with rhythms that match all combinations of host and parasite rhythms. We then test whether perturbing the availability of the best candidate nutrient in vitro changes the schedule for asexual development. Results: Our large-scale metabolomics experiment and follow up experiments reveal that only one metabolite - the amino acid isoleucine – fits criteria for a time-of-day cue used by parasites to set the schedule for replication. The response to isoleucine is a parasite strategy rather than solely the consequences of a constraint imposed by host rhythms, because unlike when parasites are deprived of other essential nutrients, they suffer no apparent costs from isoleucine withdrawal. Conclusions: Overall, our data suggest parasites can use the daily rhythmicity of blood-isoleucine concentration to synchronise asexual development with the availability of isoleucine, and potentially other resources, that arrive in the blood in a periodic manner due to the host’s daily feeding-fasting cycle. Identifying both how and why parasites keep time opens avenues for interventions; interfering with the parasite’s time-keeping mechanism may stall replication, increasing the efficacy of drugs and immune responses, and could also prevent parasites from entering dormancy to tolerate drugs.

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