The NAD interactome: identification of putative new NAD-binding proteins

Sara Duarte-Pereira; Sérgio Matos; José Luís Oliveira; Raquel M. Silva

doi:10.1007/978-3-031-17024-9_5

The NAD interactome: identification of putative new NAD-binding proteins

Sara Duarte-Pereira^*, Sérgio Matos, José Luís Oliveira, Raquel M. Silva

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Nicotinamide adenine dinucleotide (NAD) is an essential metabolite in normal cellular physiology and its deregulation may lead to several pathological conditions. NAD interacts with a vast number of proteins, acting as a coenzyme, as a substrate and regulating the interaction between proteins. The goals of this study were to characterize the proteins involved in NAD metabolism and to identify putative new NAD regulated proteins. Using an in silico approach, we first defined a NAD-binding dataset, that we characterized through pathway enrichment analysis and protein structural domains analysis. We then screened the full human proteome and further analyzed a selection of potential NAD-binding proteins. This global study of the NAD interactome resulted in the identification of new potentially NAD-binding proteins (NADPBs), including TRPC3 and a few isoforms of DGA kinases, which are involved in calcium signaling. NADBPs participate in several metabolic pathways and signaling processes in the cell, while proteins interacting with NADPBs are mostly involved in signaling pathways, including pathways related to disease, namely three major neurodegenerative diseases, Alzheimer’s, Huntington’s, and Parkinson’s.

Original language	English
Title of host publication	Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022
Editors	Florentino Fdez-Riverola, Miguel Rocha, Mohd Saberi Mohamad, Simona Caraiman, Ana Belén Gil-González
Place of Publication	Cham
Publisher	Springer Nature Switzerland AG
Pages	43-54
Number of pages	12
Volume	553
ISBN (Electronic)	9783031170249
ISBN (Print)	9783031170232
DOIs	https://doi.org/10.1007/978-3-031-17024-9_5
Publication status	Published - 2023
Event	16th International Conference on Practical Applications of Computational Biology & Bioinformatics - L'Aquila, Italy Duration: 13 Jul 2022 → 15 Jul 2022 https://www.pacbb.net/

Publication series

Name	Lecture Notes in Networks and Systems
Volume	553
ISSN (Print)	2367-3370
ISSN (Electronic)	2367-3389

Conference

Conference	16th International Conference on Practical Applications of Computational Biology & Bioinformatics
Abbreviated title	PACBB'22
Country/Territory	Italy
City	L'Aquila
Period	13/07/22 → 15/07/22
Internet address	https://www.pacbb.net/

Keywords

Nicotinamide Adenine Dinucleotide (NAD)
Protein-protein interactions (PPIs)
Protein domains

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1007/978-3-031-17024-9_5

Cite this

Duarte-Pereira, S., Matos, S., Oliveira, J. L., & Silva, R. M. (2023). The NAD interactome: identification of putative new NAD-binding proteins. In F. Fdez-Riverola, M. Rocha, M. S. Mohamad, S. Caraiman, & A. B. Gil-González (Eds.), Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022 (Vol. 553, pp. 43-54). (Lecture Notes in Networks and Systems; Vol. 553). Springer Nature Switzerland AG. https://doi.org/10.1007/978-3-031-17024-9_5

Duarte-Pereira, Sara ; Matos, Sérgio ; Oliveira, José Luís et al. / The NAD interactome : identification of putative new NAD-binding proteins. Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022. editor / Florentino Fdez-Riverola ; Miguel Rocha ; Mohd Saberi Mohamad ; Simona Caraiman ; Ana Belén Gil-González. Vol. 553 Cham : Springer Nature Switzerland AG, 2023. pp. 43-54 (Lecture Notes in Networks and Systems).

@inproceedings{3932f0c40d9544c88fe46ec1944f4291,

title = "The NAD interactome: identification of putative new NAD-binding proteins",

abstract = "Nicotinamide adenine dinucleotide (NAD) is an essential metabolite in normal cellular physiology and its deregulation may lead to several pathological conditions. NAD interacts with a vast number of proteins, acting as a coenzyme, as a substrate and regulating the interaction between proteins. The goals of this study were to characterize the proteins involved in NAD metabolism and to identify putative new NAD regulated proteins. Using an in silico approach, we first defined a NAD-binding dataset, that we characterized through pathway enrichment analysis and protein structural domains analysis. We then screened the full human proteome and further analyzed a selection of potential NAD-binding proteins. This global study of the NAD interactome resulted in the identification of new potentially NAD-binding proteins (NADPBs), including TRPC3 and a few isoforms of DGA kinases, which are involved in calcium signaling. NADBPs participate in several metabolic pathways and signaling processes in the cell, while proteins interacting with NADPBs are mostly involved in signaling pathways, including pathways related to disease, namely three major neurodegenerative diseases, Alzheimer{\textquoteright}s, Huntington{\textquoteright}s, and Parkinson{\textquoteright}s.",

keywords = "Nicotinamide Adenine Dinucleotide (NAD), Protein-protein interactions (PPIs), Protein domains",

author = "Sara Duarte-Pereira and S{\'e}rgio Matos and Oliveira, {Jos{\'e} Lu{\'i}s} and Silva, {Raquel M.}",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.; 16th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB'22 ; Conference date: 13-07-2022 Through 15-07-2022",

year = "2023",

doi = "10.1007/978-3-031-17024-9_5",

language = "English",

isbn = "9783031170232",

volume = "553",

series = "Lecture Notes in Networks and Systems",

publisher = "Springer Nature Switzerland AG",

pages = "43--54",

editor = "Florentino Fdez-Riverola and Miguel Rocha and Mohamad, {Mohd Saberi} and Simona Caraiman and Gil-Gonz{\'a}lez, {Ana Bel{\'e}n}",

booktitle = "Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022",

address = "Switzerland",

url = "https://www.pacbb.net/",

}

Duarte-Pereira, S, Matos, S, Oliveira, JL & Silva, RM 2023, The NAD interactome: identification of putative new NAD-binding proteins. in F Fdez-Riverola, M Rocha, MS Mohamad, S Caraiman & AB Gil-González (eds), Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022. vol. 553, Lecture Notes in Networks and Systems, vol. 553, Springer Nature Switzerland AG, Cham, pp. 43-54, 16th International Conference on Practical Applications of Computational Biology & Bioinformatics, L'Aquila, Italy, 13/07/22. https://doi.org/10.1007/978-3-031-17024-9_5

The NAD interactome: identification of putative new NAD-binding proteins. / Duarte-Pereira, Sara; Matos, Sérgio; Oliveira, José Luís et al.
Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022. ed. / Florentino Fdez-Riverola; Miguel Rocha; Mohd Saberi Mohamad; Simona Caraiman; Ana Belén Gil-González. Vol. 553 Cham: Springer Nature Switzerland AG, 2023. p. 43-54 (Lecture Notes in Networks and Systems; Vol. 553).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - The NAD interactome

T2 - 16th International Conference on Practical Applications of Computational Biology & Bioinformatics

AU - Duarte-Pereira, Sara

AU - Matos, Sérgio

AU - Oliveira, José Luís

AU - Silva, Raquel M.

PY - 2023

Y1 - 2023

N2 - Nicotinamide adenine dinucleotide (NAD) is an essential metabolite in normal cellular physiology and its deregulation may lead to several pathological conditions. NAD interacts with a vast number of proteins, acting as a coenzyme, as a substrate and regulating the interaction between proteins. The goals of this study were to characterize the proteins involved in NAD metabolism and to identify putative new NAD regulated proteins. Using an in silico approach, we first defined a NAD-binding dataset, that we characterized through pathway enrichment analysis and protein structural domains analysis. We then screened the full human proteome and further analyzed a selection of potential NAD-binding proteins. This global study of the NAD interactome resulted in the identification of new potentially NAD-binding proteins (NADPBs), including TRPC3 and a few isoforms of DGA kinases, which are involved in calcium signaling. NADBPs participate in several metabolic pathways and signaling processes in the cell, while proteins interacting with NADPBs are mostly involved in signaling pathways, including pathways related to disease, namely three major neurodegenerative diseases, Alzheimer’s, Huntington’s, and Parkinson’s.

AB - Nicotinamide adenine dinucleotide (NAD) is an essential metabolite in normal cellular physiology and its deregulation may lead to several pathological conditions. NAD interacts with a vast number of proteins, acting as a coenzyme, as a substrate and regulating the interaction between proteins. The goals of this study were to characterize the proteins involved in NAD metabolism and to identify putative new NAD regulated proteins. Using an in silico approach, we first defined a NAD-binding dataset, that we characterized through pathway enrichment analysis and protein structural domains analysis. We then screened the full human proteome and further analyzed a selection of potential NAD-binding proteins. This global study of the NAD interactome resulted in the identification of new potentially NAD-binding proteins (NADPBs), including TRPC3 and a few isoforms of DGA kinases, which are involved in calcium signaling. NADBPs participate in several metabolic pathways and signaling processes in the cell, while proteins interacting with NADPBs are mostly involved in signaling pathways, including pathways related to disease, namely three major neurodegenerative diseases, Alzheimer’s, Huntington’s, and Parkinson’s.

KW - Nicotinamide Adenine Dinucleotide (NAD)

KW - Protein-protein interactions (PPIs)

KW - Protein domains

UR - http://www.scopus.com/inward/record.url?scp=85142732066&partnerID=8YFLogxK

U2 - 10.1007/978-3-031-17024-9_5

DO - 10.1007/978-3-031-17024-9_5

M3 - Conference contribution

SN - 9783031170232

VL - 553

T3 - Lecture Notes in Networks and Systems

SP - 43

EP - 54

BT - Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022

A2 - Fdez-Riverola, Florentino

A2 - Rocha, Miguel

A2 - Mohamad, Mohd Saberi

A2 - Caraiman, Simona

A2 - Gil-González, Ana Belén

PB - Springer Nature Switzerland AG

CY - Cham

Y2 - 13 July 2022 through 15 July 2022

ER -

Duarte-Pereira S, Matos S, Oliveira JL, Silva RM. The NAD interactome: identification of putative new NAD-binding proteins. In Fdez-Riverola F, Rocha M, Mohamad MS, Caraiman S, Gil-González AB, editors, Practical Applications of Computational Biology and Bioinformatics, 16th International Conference, PACBB 2022. Vol. 553. Cham: Springer Nature Switzerland AG. 2023. p. 43-54. (Lecture Notes in Networks and Systems). doi: 10.1007/978-3-031-17024-9_5

The NAD interactome: identification of putative new NAD-binding proteins

Abstract

Publication series

Conference

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

InDig: Innovation and digital teaching technologies in Dental Medicine

CIIS: Center for Interdisciplinary Research in Health

Cite this

The NAD interactome: identification of putative new NAD-binding proteins

Abstract

Publication series

Conference

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Projects

InDig: Innovation and digital teaching technologies in Dental Medicine

CIIS: Center for Interdisciplinary Research in Health

Cite this