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Article ; Online: Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS

Babar, Vasudeo / Sharma, Sitansh / Shaikh, Abdul Rajjak / Oliva, Romina / Chawla, Mohit / Cavallo, Luigi

ACS applied materials & interfaces

2024 Volume 16, Issue 17, Page(s) 21427–21437

Abstract: In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA ... ...

Abstract	In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS
MeSH term(s)	Molybdenum/chemistry ; Disulfides/chemistry ; DNA/chemistry ; Adsorption ; Density Functional Theory
Chemical Substances	Molybdenum (81AH48963U) ; Disulfides ; molybdenum disulfide (ZC8B4P503V) ; DNA (9007-49-2)
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c18400
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Article ; Online: Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.

Chawla, Mohit / Kalra, Kanav / Cao, Zhen / Cavallo, Luigi / Oliva, Romina

Nucleic acids research

2022 Volume 50, Issue 20, Page(s) 11455–11469

Abstract: We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning ... ...

Abstract	We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
Language	English
Publishing date	2022-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac1081
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Article ; Online: Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.

Barradas-Bautista, Didier / Almajed, Ali / Oliva, Romina / Kalnis, Panos / Cavallo, Luigi

Bioinformatics advances

2023 Volume 3, Issue 1, Page(s) vbad012

Abstract: Motivation: Protein-protein interactions drive many relevant biological events, such as infection, replication and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D ... ...

Abstract	Motivation: Protein-protein interactions drive many relevant biological events, such as infection, replication and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D structures. However, such experiments take time and are expensive; moreover, the current technology cannot keep up with the high discovery rate of new interactions. Computational modeling, like protein-protein docking, can help to fill this gap by generating docking poses. Protein-protein docking generally consists of two parts, sampling and scoring. The sampling is an exhaustive search of the tridimensional space. The caveat of the sampling is that it generates a large number of incorrect poses, producing a highly unbalanced dataset. This limits the utility of the data to train machine learning classifiers. Results: Using weak supervision, we developed a data augmentation method that we named hAIkal. Using hAIkal, we increased the labeled training data to train several algorithms. We trained and obtained different classifiers; the best classifier has 81% accuracy and 0.51 Matthews' correlation coefficient on the test set, surpassing the state-of-the-art scoring functions. Availability and implementation: Docking models from Benchmark 5 are available at https://doi.org/10.5281/zenodo.4012018. Processed tabular data are available at https://repository.kaust.edu.sa/handle/10754/666961. Google colab is available at https://colab.research.google.com/drive/1vbVrJcQSf6\_C3jOAmZzgQbTpuJ5zC1RP?usp=sharing. Supplementary information: Supplementary data are available at
Language	English
Publishing date	2023-02-02
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad012
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Article ; Online: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly

Cavallo, Luigi / Oliva, Romina

bioRxiv

Abstract: The iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming ...

Abstract	The iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21st, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the “fusion core” of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29th, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.06.08.140152
Database	COVID19

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Article ; Online: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly

Cavallo, Luigi / Oliva, Romina

bioRxiv

Abstract: The iconic 9red crown9 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming ...

Abstract	The iconic 9red crown9 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21st, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the 9fusion core9 of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29th, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly.
Keywords	covid19
Language	English
Publishing date	2020-06-09
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.06.08.140152
Database	COVID19

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Book ; Online: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly

Cavallo, Luigi / Oliva, Romina

2020

Abstract: AbstractThe iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was ... ...

Abstract	AbstractThe iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21$^{st}/$$, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the “fusion core” of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29$^{th}$$, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly. We gratefully acknowledge all the Authors from the Originating laboratories responsible for obtaining the specimens and the Submitting laboratories where genetic sequence data were generated and shared via the GISAID Initiative, on which this research is based. R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attività Base di Ricerca) for funding; L.C. acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources.
Keywords	covid19
Subject code	500
Publishing date	2020-06-09
Publisher	Cold Spring Harbor Laboratory
Publishing country	sa
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Toward α-1,3/4 fucosyltransferases targeted drug discovery: In silico uncovering of promising natural inhibitors of fucosyltransferase 6.

Magdaleno, Jorge Samuel Leon / Grewal, Ravneet K / Medina-Franco, José L / Oliva, Romina / Shaikh, Abdul Rajjak / Cavallo, Luigi / Chawla, Mohit

Journal of cellular biochemistry

2023 Volume 124, Issue 8, Page(s) 1173–1185

Abstract: Sialyl Lewis X ( ... ...

Abstract	Sialyl Lewis X (sLe
MeSH term(s)	Humans ; Male ; Drug Discovery ; Fucosyltransferases/antagonists & inhibitors ; Fucosyltransferases/metabolism ; Glycosylation ; Neoplasms ; Sialyl Lewis X Antigen/metabolism
Chemical Substances	Fucosyltransferases (EC 2.4.1.-) ; Sialyl Lewis X Antigen
Language	English
Publishing date	2023-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.30440
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Article ; Online: The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses.

Barradas-Bautista, Didier / Cao, Zhen / Cavallo, Luigi / Oliva, Romina

BMC bioinformatics

2020 Volume 21, Issue Suppl 8, Page(s) 262

Abstract: Background: Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind docking experiment. We introduced ...

Abstract	Background: Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind docking experiment. We introduced in the field CONSRANK (CONSensus RANKing), the first pure consensus method. Also available as a web server, CONSRANK ranks docking models in an ensemble based on their ability to match the most frequent inter-residue contacts in it. We have been blindly testing CONSRANK in all the latest CAPRI rounds, where we showed it to perform competitively with the state-of-the-art energy and knowledge-based scoring functions. More recently, we developed Clust-CONSRANK, an algorithm introducing a contact-based clustering of the models as a preliminary step of the CONSRANK scoring process. In the latest CASP13-CAPRI joint experiment, we participated as scorers with a novel pipeline, combining both our scoring tools, CONSRANK and Clust-CONSRANK, with our interface analysis tool COCOMAPS. Selection of the 10 models for submission was guided by the strength of the emerging consensus, and their final ranking was assisted by results of the interface analysis. Results: As a result of the above approach, we were by far the first scorer in the CASP13-CAPRI top-1 ranking, having high/medium quality models ranked at the top-1 position for the majority of targets (11 out of the total 19). We were also the first scorer in the top-10 ranking, on a par with another group, and the second scorer in the top-5 ranking. Further, we topped the ranking relative to the prediction of binding interfaces, among all the scorers and predictors. Using the CASP13-CAPRI targets as case studies, we illustrate here in detail the approach we adopted. Conclusions: Introducing some flexibility in the final model selection and ranking, as well as differentiating the adopted scoring approach depending on the targets were the key assets for our highly successful performance, as compared to previous CAPRI rounds. The approach we propose is entirely based on methods made available to the community and could thus be reproduced by any user.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Humans ; Protein Binding/genetics ; Protein Conformation ; Protein Interaction Mapping/methods ; Proteins/chemistry
Chemical Substances	Proteins
Language	English
Publishing date	2020-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-020-03600-8
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Article ; Online: Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.

Kalra, Kanav / Gorle, Suresh / Cavallo, Luigi / Oliva, Romina / Chawla, Mohit

Nucleic acids research

2020 Volume 48, Issue 11, Page(s) 5825–5838

Abstract: We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. ...

Abstract	We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.
MeSH term(s)	Molecular Dynamics Simulation ; Oxygen/chemistry ; Quantum Theory ; RNA/chemistry ; Thermodynamics ; Water/chemistry
Chemical Substances	Water (059QF0KO0R) ; RNA (63231-63-0) ; Oxygen (S88TT14065)
Language	English
Publishing date	2020-05-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa345
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Article ; Online: A random forest classifier for protein-protein docking models.

Barradas-Bautista, Didier / Cao, Zhen / Vangone, Anna / Oliva, Romina / Cavallo, Luigi

Bioinformatics advances

2021 Volume 2, Issue 1, Page(s) vbab042

Abstract: Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein-protein complexes obtained by popular docking software. To this aim, we generated : Supplementary information: Supplementary ... ...

Abstract	Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein-protein complexes obtained by popular docking software. To this aim, we generated Supplementary information: Supplementary data are available at Software and data availability statement: The docking models are available at https://doi.org/10.5281/zenodo.4012018. The programs underlying this article will be shared on request to the corresponding authors.
Language	English
Publishing date	2021-12-10
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbab042
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