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Article ; Online: Multicystic Hepatic Lesion: An Unusual Presentation of Extra-Pulmonary Tuberculosis in a Child.

Kumar, Pawan / Sharma, Sudha / Banerjee, Avik

2021 Volume 58, Issue 5, Page(s) 485–486

MeSH term(s)	Child ; Family ; Humans ; Tuberculosis ; Tuberculosis, Pulmonary/diagnosis
Language	English
Publishing date	2021-05-12
Publishing country	India
Document type	Case Reports ; Journal Article
ZDB-ID	402594-5
ISSN	0974-7559 ; 0019-6061
ISSN (online)	0974-7559
ISSN	0019-6061
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Article ; Online: Erasure Tolerant Quantum Memory and the Quantum Null Energy Condition in Holographic Systems.

Banerjee, Avik / Kibe, Tanay / Mittal, Nehal / Mukhopadhyay, Ayan / Roy, Pratik

Physical review letters

2022 Volume 129, Issue 19, Page(s) 191601

Abstract: Investigating principles for storage of quantum information at finite temperature with minimal need for active error correction is an active area of research. We bear upon this question in two-dimensional holographic conformal field theories via the ... ...

Abstract	Investigating principles for storage of quantum information at finite temperature with minimal need for active error correction is an active area of research. We bear upon this question in two-dimensional holographic conformal field theories via the quantum null energy condition that we have shown earlier to implement the restrictions imposed by quantum thermodynamics on such many-body systems. We study an explicit encoding of a logical qubit into two similar chirally propagating excitations of finite von Neumann entropy on a finite temperature background whose erasure can be implemented by an appropriate inhomogeneous and instantaneous energy-momentum inflow from an infinite energy memoryless bath due to which the system transits to a thermal state. Holographically, these fast erasure processes can be depicted by generalized AdS-Vaidya geometries described previously in which no assumption of specific form of bulk matter is needed. We show that the quantum null energy condition gives analytic results for the minimal finite temperature needed for the deletion which is larger than the initial background temperature in consistency with Landauer's principle. In particular, we find a simple expression for the minimum final temperature needed for the erasure of a large number of encoding qubits. We also find that if the encoding qubits are localized over an interval shorter than a specific localization length, then the fast erasure process is impossible, and furthermore this localization length is the largest for an optimal amount of encoding qubits determined by the central charge. We estimate the optimal encoding qubits for realistic protection against fast erasure. We discuss possible generalizations of our study for novel constructions of fault-tolerant quantum gates operating at finite temperature.
Language	English
Publishing date	2022-11-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.129.191601
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Article ; Online: A general computational design strategy for stabilizing viral class I fusion proteins.

Gonzalez, Karen J / Huang, Jiachen / Criado, Miria F / Banerjee, Avik / Tompkins, Stephen M / Mousa, Jarrod J / Strauch, Eva-Maria

Nature communications

2024 Volume 15, Issue 1, Page(s) 1335

Abstract: Many pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an ... ...

Abstract	Many pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more stable postfusion state. Mounting evidence underscores that antibodies targeting the prefusion conformation are the most potent, making it a compelling vaccine candidate. Here, we establish a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. With this protocol, we stabilize the fusion proteins of the RSV, hMPV, and SARS-CoV-2 viruses, testing fewer than a handful of designs. The solved structures of these designed proteins from all three viruses evidence the atomic accuracy of our approach. Furthermore, the humoral response of the redesigned RSV F protein compares to that of the recently approved vaccine in a mouse model. While the parallel design of two conformations allows the identification of energetically sub-optimal positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
MeSH term(s)	Animals ; Mice ; Viral Fusion Proteins ; Antibodies, Neutralizing ; Antibodies, Viral ; Vaccines ; Protein Conformation
Chemical Substances	Viral Fusion Proteins ; Antibodies, Neutralizing ; Antibodies, Viral ; Vaccines
Language	English
Publishing date	2024-02-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45480-z
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Article: A general computational design strategy for stabilizing viral class I fusion proteins.

Gonzalez, Karen J / Huang, Jiachen / Criado, Miria F / Banerjee, Avik / Tompkins, Stephen / Mousa, Jarrod J / Strauch, Eva-Maria

bioRxiv : the preprint server for biology

2023

Abstract: Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible ... ...

Abstract	Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more favorable and stable postfusion state. An increasing amount of evidence exists highlighting that antibodies targeting the prefusion conformation are the most potent. However, many mutations have to be evaluated before identifying prefusion-stabilizing substitutions. We therefore established a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. As a proof of concept, we applied this principle to the fusion protein of the RSV, hMPV, and SARS-CoV-2 viruses. For each protein, we tested less than a handful of designs to identify stable versions. Solved structures of designed proteins from the three different viruses evidenced the atomic accuracy of our approach. Furthermore, the immunological response of the RSV F design compared to a current clinical candidate in a mouse model. While the parallel design of two conformations allows identifying and selectively modifying energetically less optimized positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. We recaptured many approaches previously introduced manually for the stabilization of viral surface proteins, such as cavity-filling, optimization of polar interactions, as well as postfusion-disruptive strategies. Using our approach, it is possible to focus on the most impacting mutations and potentially preserve the immunogen as closely as possible to its native version. The latter is important as sequence re-design can cause perturbations to B and T cell epitopes. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
Language	English
Publishing date	2023-03-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.16.532924
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Article: Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands.

Abdelkarim, Hazem / Hitchinson, Ben / Banerjee, Avik / Gaponenko, Vadim

Advances in experimental medicine and biology

2019 Volume 1163, Page(s) 171–186

Abstract: NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant ... ...

Abstract	NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant advantage for discovery and characterization of allosteric effects. These effects are observed when binding at one site of the protein affects another distinct site through conformational transitions. Allosteric regulation of proteins has been observed in multiple physiological processes in health and disease, providing an opportunity for the development of allosteric inhibitors. These compounds do not directly interact with the orthosteric site of the protein but influence its structure and function. In this book chapter, we provide an overview on how NMR methods are utilized to identify allosteric sites and to discover novel inhibitors, highlighting examples from the field. We also describe how NMR has contributed to understanding of allosteric mechanisms and propose that it is likely to play an important role in clarification and further development of key concepts of allostery.
MeSH term(s)	Allosteric Regulation ; Allosteric Site ; Binding Sites ; Drug Discovery/methods ; Drug Discovery/trends ; Ligands ; Magnetic Resonance Spectroscopy ; Protein Conformation
Chemical Substances	Ligands
Language	English
Publishing date	2019-10-31
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-981-13-8719-7_8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The dynamic nature of the K-Ras/calmodulin complex can be altered by oncogenic mutations.

Abdelkarim, Hazem / Leschinsky, Nicholas / Jang, Hyunbum / Banerjee, Avik / Nussinov, Ruth / Gaponenko, Vadim

Current opinion in structural biology

2021 Volume 71, Page(s) 164–170

Abstract: Oncogenic mutant K-Ras promotes cancer cell proliferation, migration, invasion, and survival by assembling signaling complexes. To date, the functional and structural roles of K-Ras mutations within these complexes are incompletely understood despite ... ...

Abstract	Oncogenic mutant K-Ras promotes cancer cell proliferation, migration, invasion, and survival by assembling signaling complexes. To date, the functional and structural roles of K-Ras mutations within these complexes are incompletely understood despite their mechanistic and therapeutic significance. Here, we review recent advances in understanding specific binding between K-Ras and the calcium sensor calmodulin. This interaction positively and negatively regulates diverse functions of K-Ras in cancer, suggesting flexibility in K-Ras/calmodulin complex formation. Also, structural data suggest that oncogenic K-Ras likely samples several conformational states, influencing its distinct assemblies with calmodulin and with other proteins. Understanding how K-Ras interacts with calmodulin and with other partners is essential to discovering novel inhibitors of K-Ras in cancer.
MeSH term(s)	Calcium/metabolism ; Calmodulin/genetics ; Calmodulin/metabolism ; Humans ; Mutation ; Neoplasms/genetics ; Proto-Oncogene Proteins p21(ras) ; Signal Transduction
Chemical Substances	Calmodulin ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2021-07-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2021.06.008
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Article ; Online: Screening of the Medicines for Malaria Venture Pandemic Response Box for Discovery of Antivirulent Drug against Pseudomonas aeruginosa.

Macho, Markéta / Saha, Subhasish / Konert, Grzegorz / Banerjee, Avik / Ewe, Daniela / Hrouzek, Pavel / Urajová, Petra / Saurav, Kumar

Microbiology spectrum

2022 , Page(s) e0223222

Abstract: Resistance development and exhaustion of the arsenal of existing antibacterial agents urgently require an alternative approach toward drug discovery. Herein, we report the screening of Medicines for Malaria Venture (MMV) Pandemic Response Box (PRB) ... ...

Abstract	Resistance development and exhaustion of the arsenal of existing antibacterial agents urgently require an alternative approach toward drug discovery. Herein, we report the screening of Medicines for Malaria Venture (MMV) Pandemic Response Box (PRB) through a cascade developed to streamline the potential compounds with antivirulent properties to combat an opportunistic pathogen, Pseudomonas aeruginosa. To find an agent suppressing the production of P. aeruginosa virulence factors, we assessed the potential of the compounds in PRB with quorum sensing inhibitory activity. Our approach led us to identify four compounds with significant inhibition of extracellular virulence factor production and biofilm formation. This provides an opportunity to expand and redirect the application of these data sets toward the development of a drug with unexplored target-based activity.
Language	English
Publishing date	2022-10-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02232-22
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Article ; Online: An insight to the conserved water mediated dynamics of catalytic His88 and its recognition to thyroxin and RBP binding residues in human transthyretin.

Banerjee, Avik / Mukhopadhyay, Bishnu P

Journal of biomolecular structure & dynamics

2015 Volume 33, Issue 9, Page(s) 1973–1988

Abstract: Human transthyretin (hTTR) is a multifunctional protein involved in several amyloidogenic diseases. Besides transportation of thyroxin and vitamin-A, its role towards the catalysis of apolipoprotein-A1 and Aβ-peptide are also drawing interest. The role ... ...

Abstract	Human transthyretin (hTTR) is a multifunctional protein involved in several amyloidogenic diseases. Besides transportation of thyroxin and vitamin-A, its role towards the catalysis of apolipoprotein-A1 and Aβ-peptide are also drawing interest. The role of water molecules in the catalytic mechanism is still unknown. Extensive analyses of 14 high-resolution X-ray structures of human transthyretin and MD simulation studies have revealed the presence of eight conserved hydrophilic centres near its catalytic zone which may be indispensable for the function, dynamics and stability of the protein. Three water molecules (W1, W2 and W3) form a cluster and play an important role in the recognition of the catalytic and RBP-binding residues. They also induce the reorganisation of the His88 for coupling with other catalytic residues (His90, Glu92). Another water molecule (W5) participate in inter-monomer recognition between the catalytic and thyroxin binding sites. The rest four water molecules (W6, W*, W(#) and W(†)) form a distorted tetrahedral cluster and impart stability to the catalytic core of hTTR. The conserved water mediated recognition dynamics of the different functional sites may provide some rational clues towards the understanding of the activity and mechanism of hTTR.
MeSH term(s)	Apolipoproteins A/chemistry ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Histidine/chemistry ; Histidine/genetics ; Humans ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Prealbumin/chemistry ; Prealbumin/metabolism ; Protein Structure, Tertiary ; Thyroxine/chemistry ; Vitamin A/chemistry ; Vitamin A/metabolism ; Water/chemistry
Chemical Substances	Apolipoproteins A ; Prealbumin ; Water (059QF0KO0R) ; Vitamin A (11103-57-4) ; Histidine (4QD397987E) ; Thyroxine (Q51BO43MG4)
Language	English
Publishing date	2015-09
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2014.984632
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Article ; Online: NMR resonance assignment and structure prediction of the C-terminal domain of the microtubule end-binding protein 3.

Abdelkarim, Hazem / Hitchinson, Ben / Qu, Xinyan / Banerjee, Avik / Komarova, Yulia A / Gaponenko, Vadim

PloS one

2020 Volume 15, Issue 5, Page(s) e0232338

Abstract: End-binding proteins (EBs) associate with the growing microtubule plus ends to regulate microtubule dynamics as well as the interaction with intracellular structures. EB3 contributes to pathological vascular leakage through interacting with the inositol ... ...

Abstract	End-binding proteins (EBs) associate with the growing microtubule plus ends to regulate microtubule dynamics as well as the interaction with intracellular structures. EB3 contributes to pathological vascular leakage through interacting with the inositol 1,4,5-trisphosphate receptor 3 (IP3R3), a calcium channel located at the endoplasmic reticulum membrane. The C-terminal domain of EB3 (residues 200-281) is functionally important for this interaction because it contains the effector binding sites, a prerequisite for EB3 activity and specificity. Structural data for this domain is limited. Here, we report the backbone chemical shift assignments for the human EB3 C-terminal domain and computationally explore its EB3 conformations. Backbone assignments, along with computational models, will allow future investigation of EB3 structural dynamics, interactions with effectors, and will facilitate the development of novel EB3 inhibitors.
MeSH term(s)	Humans ; Microtubule-Associated Proteins/chemistry ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Domains ; Protein Structure, Secondary
Chemical Substances	MAPRE3 protein, human ; Microtubule-Associated Proteins
Language	English
Publishing date	2020-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0232338
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Article ; Online: A general computational design strategy for stabilizing viral class I fusion proteins

Gonzalez, Karen J / Huang, Jiachen / Criado, Miria F / Banerjee, Avik / Tompkins, Stephen Mark / Mousa, Jarrod J / Strauch, Eva Maria

bioRxiv

Abstract	Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more favorable and stable postfusion state. An increasing amount of evidence exists highlighting that antibodies targeting the prefusion conformation are the most potent. However, many mutations have to be evaluated before identifying prefusion-stabilizing substitutions. We therefore established a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. As a proof of concept, we applied this principle to the fusion protein of the RSV, hMPV, and SARS-CoV-2 viruses. For each protein, we tested less than a handful of designs to identify stable versions. Solved structures of designed proteins from the three different viruses evidenced the atomic accuracy of our approach. Furthermore, the immunological response of the RSV F design compared to a current clinical candidate in a mouse model. While the parallel design of two conformations allows identifying and selectively modifying energetically less optimized positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. We recaptured many approaches previously introduced manually for the stabilization of viral surface proteins, such as cavity-filling, optimization of polar interactions, as well as postfusion-disruptive strategies. Using our approach, it is possible to focus on the most impacting mutations and potentially preserve the immunogen as closely as possible to its native version. The latter is important as sequence re-design can cause perturbations to B and T cell epitopes. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
Keywords	covid19
Language	English
Publishing date	2023-03-17
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.03.16.532924
Database	COVID19

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