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Article ; Online: Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation.

Amangeldina, Aidana / Tan, Zhen Wah / Berezovsky, Igor N

Current research in structural biology

2024 Volume 7, Page(s) 100129

Abstract: Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in ... ...

Abstract	Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.
Language	English
Publishing date	2024-02-01
Publishing country	Netherlands
Document type	Journal Article
ISSN	2665-928X
ISSN (online)	2665-928X
DOI	10.1016/j.crstbi.2024.100129
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Learning About Allosteric Drugs and Ways to Design Them.

Wah Tan, Zhen / Tee, Wei-Ven / Berezovsky, Igor N

Journal of molecular biology

2022 Volume 434, Issue 17, Page(s) 167692

Abstract: While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. ... ...

Abstract	While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required drug efficacy. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
MeSH term(s)	Allosteric Regulation/drug effects ; Allosteric Site ; Binding Sites ; Drug Design ; Ligands ; Proteins/chemistry
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2022-06-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167692
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Article ; Online: Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia.

Tan, Zhen Wah / Toong, Ping Jing / Guarnera, Enrico / Berezovsky, Igor N

Scientific reports

2023 Volume 13, Issue 1, Page(s) 5906

Abstract: We tackle here genomic mechanisms of a rapid onset and recovery from anosmia-a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin ... ...

Abstract	We tackle here genomic mechanisms of a rapid onset and recovery from anosmia-a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin structure in mice, we hypothesized that the disruption of the OR gene expression and, respectively, deficiency of the OR function can be caused by chromatin reorganization taking place upon SARS-CoV-2 infection. We obtained chromatin ensemble reconstructions from COVID-19 patients and control samples using our original computational framework for the whole-genome 3D chromatin ensemble reconstruction. Specifically, we used megabase-scale structural units and effective interactions between them obtained in the Markov State modelling of the Hi-C contact network as an unput in the stochastic embedding procedure of the whole-genome 3D chromatin ensemble reconstruction. We have also developed here a new procedure for analyzing fine structural hierarchy with (sub)TAD-size units in local chromatin regions, which we apply here to parts of chromosomes containing OR genes and corresponding regulatory elements. We observed structural modifications in COVID-19 patients on different levels of chromatin organization, from the alteration of whole genome structure and chromosomal intermingling to reorganization of contacts between chromatin loops at the level of topologically associating domains. While complementary data on known regulatory elements point to potential pathology-associated changes within the overall picture of chromatin alterations, further investigation using additional epigenetic factors mapped on 3D reconstructions with improved resolution will be required for better understanding of anosmia caused by SARS-CoV-2 infection.
MeSH term(s)	Animals ; Mice ; Chromatin ; Olfactory Receptor Neurons ; Anosmia ; COVID-19/genetics ; SARS-CoV-2/genetics ; Chromosomes
Chemical Substances	Chromatin
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-32896-8
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Article ; Online: Learning About Allosteric Drugs and Ways to Design Them

Wah Tan, Zhen / Tee, Wei-Ven / Berezovsky, Igor N.

Journal of Molecular Biology. 2022 Sept., v. 434, no. 17 p.167692-

2022

Abstract	While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required drug efficacy. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
Keywords	drugs ; ligands ; molecular biology ; precision medicine ; protein kinases ; drug design ; allosteric sites ; allosteric drugs ; allosteric mutations
Language	English
Dates of publication	2022-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167692
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Article ; Online: Disrupted chromatin architecture in olfactory sensory neurons

Zhen Wah Tan / Ping Jing Toong / Enrico Guarnera / Igor N. Berezovsky

Scientific Reports, Vol 13, Iss 1, Pp 1-

looking for the link from COVID-19 infection to anosmia

2023 Volume 15

Abstract: Abstract We tackle here genomic mechanisms of a rapid onset and recovery from anosmia—a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via ... ...

Abstract	Abstract We tackle here genomic mechanisms of a rapid onset and recovery from anosmia—a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin structure in mice, we hypothesized that the disruption of the OR gene expression and, respectively, deficiency of the OR function can be caused by chromatin reorganization taking place upon SARS-CoV-2 infection. We obtained chromatin ensemble reconstructions from COVID-19 patients and control samples using our original computational framework for the whole-genome 3D chromatin ensemble reconstruction. Specifically, we used megabase-scale structural units and effective interactions between them obtained in the Markov State modelling of the Hi-C contact network as an unput in the stochastic embedding procedure of the whole-genome 3D chromatin ensemble reconstruction. We have also developed here a new procedure for analyzing fine structural hierarchy with (sub)TAD-size units in local chromatin regions, which we apply here to parts of chromosomes containing OR genes and corresponding regulatory elements. We observed structural modifications in COVID-19 patients on different levels of chromatin organization, from the alteration of whole genome structure and chromosomal intermingling to reorganization of contacts between chromatin loops at the level of topologically associating domains. While complementary data on known regulatory elements point to potential pathology-associated changes within the overall picture of chromatin alterations, further investigation using additional epigenetic factors mapped on 3D reconstructions with improved resolution will be required for better understanding of anosmia caused by SARS-CoV-2 infection.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Three-dimensional chromatin ensemble reconstruction via stochastic embedding.

Guarnera, Enrico / Tan, Zhen Wah / Berezovsky, Igor N

Structure (London, England : 1993)

2021 Volume 29, Issue 6, Page(s) 622–634.e3

Abstract: We propose a comprehensive method for reconstructing the whole-genome chromatin ensemble from the Hi-C data. The procedure starts from Markov state modeling (MSM), delineating the structural hierarchy of chromatin organization with partitioning and ... ...

Abstract	We propose a comprehensive method for reconstructing the whole-genome chromatin ensemble from the Hi-C data. The procedure starts from Markov state modeling (MSM), delineating the structural hierarchy of chromatin organization with partitioning and effective interactions archetypal for corresponding levels of hierarchy. The stochastic embedding procedure introduced in this work provides the 3D ensemble reconstruction, using effective interactions obtained by the MSM as the input. As a result, we obtain the structural ensemble of a genome, allowing one to model the functional and the cell-type variability in the chromatin structure. The whole-genome reconstructions performed on the human B lymphoblastoid (GM12878) and lung fibroblast (IMR90) Hi-C data unravel distinctions in their morphologies and in the spatial arrangement of intermingling chromosomal territories, paving the way to studies of chromatin dynamics, developmental changes, and conformational transitions taking place in normal cells and during potential pathological developments.
MeSH term(s)	Cell Line ; Chromatin/chemistry ; Computational Biology/methods ; Epigenesis, Genetic ; Female ; Genome, Human ; Humans ; Markov Chains ; Models, Molecular ; Molecular Conformation ; Stochastic Processes
Chemical Substances	Chromatin
Language	English
Publishing date	2021-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.01.008
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Article ; Online: Correction to: Predicting Coronary Artery Disease in Primary Care: Development and Validation of a Diagnostic Risk Score for Major Ethnic Groups in Southeast Asia.

Wang, Zhen Sinead / Yap, Jonathan / Koh, Yi Ling Eileen / Chia, Shaw Yang / Nivedita, N / Ang, Teck Wee Andrew / Goh, Soo Chye Paul / Lee, Cia Sin / Tan, Lee Lim Joanna / Ooi, Chai Wah / Seow, Matthew / Yeo, Khung Keong / Chua, Siang Jin Terrance / Tan, Ngiap Chuan

Journal of general internal medicine

2024

Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Published Erratum
ZDB-ID	639008-0
ISSN	1525-1497 ; 0884-8734
ISSN (online)	1525-1497
ISSN	0884-8734
DOI	10.1007/s11606-024-08684-z
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Article ; Online: AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design.

Tan, Zhen Wah / Tee, Wei-Ven / Guarnera, Enrico / Berezovsky, Igor N

Nucleic acids research

2022 Volume 51, Issue D1, Page(s) D345–D351

Abstract: AlloMAPS 2 is an update of the Allosteric Mutation Analysis and Polymorphism of Signalling database, which contains data on allosteric communication obtained for predicted structures in the AlphaFold database (AFDB) and trRosetta-predicted Pfam domains. ... ...

Abstract	AlloMAPS 2 is an update of the Allosteric Mutation Analysis and Polymorphism of Signalling database, which contains data on allosteric communication obtained for predicted structures in the AlphaFold database (AFDB) and trRosetta-predicted Pfam domains. The data update contains Allosteric Signalling Maps (ASMs) and Allosteric Probing Maps (APMs) quantifying allosteric effects of mutations and of small probe binding, respectively. To ensure quality of the ASMs and APMs, we performed careful and accurate selection of protein sets containing high-quality predicted structures in both databases for each organism/structure, and the data is available for browsing and download. The data for remaining structures are available for download and should be used at user's discretion and responsibility. We believe these massive data can facilitate both diagnostics and drug design within the precision medicine paradigm. Specifically, it can be instrumental in the analysis of allosteric effects of pathological and rescue mutations, providing starting points for fragment-based design of allosteric effectors. The exhaustive character of allosteric signalling and probing fingerprints will be also useful in future developments of corresponding machine learning applications. The database is freely available at: http://allomaps.bii.a-star.edu.sg.
MeSH term(s)	Allosteric Regulation/genetics ; Proteins/chemistry ; Mutation ; Signal Transduction ; Drug Design ; Databases, Protein
Chemical Substances	Proteins
Language	English
Publishing date	2022-09-27
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/gkac828
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Article ; Online: Conservation and Diversity in Allosteric Fingerprints of Proteins for Evolutionary-inspired Engineering and Design.

Tee, Wei-Ven / Tan, Zhen Wah / Guarnera, Enrico / Berezovsky, Igor N

Journal of molecular biology

2022 Volume 434, Issue 17, Page(s) 167577

Abstract: Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for ... ...

Abstract	Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order-disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.
MeSH term(s)	Allosteric Regulation/drug effects ; Biological Products/chemistry ; Biological Products/pharmacology ; Drug Design ; Protein Domains ; Proteins/chemistry ; Proteins/genetics
Chemical Substances	Biological Products ; Proteins
Language	English
Publishing date	2022-04-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167577
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Article ; Online: Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein.

Tan, Zhen Wah / Tee, Wei-Ven / Samsudin, Firdaus / Guarnera, Enrico / Bond, Peter J / Berezovsky, Igor N

Structure (London, England : 1993)

2022 Volume 30, Issue 4, Page(s) 590–607.e4

Abstract: Recent developments in the SARS-CoV-2 pandemic point to its inevitable transformation into an endemic disease, urging both refinement of diagnostics for emerging variants of concern (VOCs) and design of variant-specific drugs in addition to vaccine ... ...

Abstract	Recent developments in the SARS-CoV-2 pandemic point to its inevitable transformation into an endemic disease, urging both refinement of diagnostics for emerging variants of concern (VOCs) and design of variant-specific drugs in addition to vaccine adjustments. Exploring the structure and dynamics of the SARS-CoV-2 Spike protein, we argue that the high-mutability characteristic of RNA viruses coupled with the remarkable flexibility and dynamics of viral proteins result in a substantial involvement of allosteric mechanisms. While allosteric effects of mutations should be considered in predictions and diagnostics of new VOCs, allosteric drugs advantageously avoid escape mutations via non-competitive inhibition originating from alternative distal locations. The exhaustive allosteric signaling and probing maps presented herein provide a comprehensive picture of allostery in the spike protein, making it possible to locate potential mutations that could work as new VOC "drivers" and to determine binding patches that may be targeted by newly developed allosteric drugs.
MeSH term(s)	COVID-19/drug therapy ; Humans ; Mutation ; Pandemics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.12.011
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