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Article ; Online: Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity

Sergeeva, Alina P. / Katsamba, Phinikoula S. / Liao, Junzhuo / Sampson, Jared M. / Bahna, Fabiana / Mannepalli, Seetha / Morano, Nicholas C. / Shapiro, Lawrence / Friesner, Richard A. / Honig, Barry

Journal of Molecular Biology. 2023 Aug., v. 435, no. 15 p.168187-

2023

Abstract: The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations ... ...

Abstract	The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used. Overall, we find that FEP performance is superior to that of other computational approaches examined as determined by agreement with experiment and, in particular, by its ability to identify stabilizing mutations. Moreover, the calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in Omicron variants and offer a physical explanation for the underlying mechanism. Overall, our results suggest that despite the significant computational cost, FEP calculations may offer an effective strategy to understand the effects of interfacial mutations on protein–protein binding affinities and, hence, in a variety of practical applications such as the optimization of neutralizing antibodies.
Keywords	Gibbs free energy ; Severe acute respiratory syndrome coronavirus 2 ; enzymes ; humans ; molecular biology ; mutants ; mutation ; surface plasmon resonance ; viruses ; FEP ; SPR ; protein–protein interactions ; ddG prediction ; receptor binding domain and angiotensin converting enzyme 2
Language	English
Dates of publication	2023-08
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.2023.168187
Database	NAL-Catalogue (AGRICOLA)

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Article: Astrocyte morphogenesis requires self-recognition.

Zipursky, S / Lee, John / Sergeeva, Alina / Ahlsen, Goran / Mannepalli, Seetha / Bahna, Fabiana / Goodman, Kerry / Khakh, Baljit / Weiner, Joshua / Shapiro, Lawrence / Honig, Barry

Research square

2024

Abstract: Self-recognition is a fundamental cellular process across evolution and forms the basis of neuronal self-avoidance1-4. Clustered protocadherins (Pcdh), comprising a large family of isoform-specific homophilic recognition molecules, play a pivotal role in ...

Abstract	Self-recognition is a fundamental cellular process across evolution and forms the basis of neuronal self-avoidance1-4. Clustered protocadherins (Pcdh), comprising a large family of isoform-specific homophilic recognition molecules, play a pivotal role in neuronal self-avoidance required for mammalian brain development5-7. The probabilistic expression of different Pcdh isoforms confers unique identities upon neurons and forms the basis for neuronal processes to discriminate between self and non-self5,6,8. Whether this self-recognition mechanism exists in astrocytes, the other predominant cell type of the brain, remains unknown. Here, we report that a specific isoform in the Pcdhγ cluster, γC3, is highly enriched in human and murine astrocytes. Through genetic manipulation, we demonstrate that γC3 acts autonomously to regulate astrocyte morphogenesis in the mouse visual cortex. To determine if γC3 proteins act by promoting recognition between processes of the same astrocyte, we generated pairs of γC3 chimeric proteins capable of heterophilic binding to each other, but incapable of homophilic binding. Co-expressing complementary heterophilic binding isoform pairs in the same γC3 null astrocyte restored normal morphology. By contrast, chimeric γC3 proteins individually expressed in single γC3 null mutant astrocytes did not. These data establish that self-recognition is essential for astrocyte development in the mammalian brain and that, by contrast to neuronal self-recognition, a single Pcdh isoform is both necessary and sufficient for this process.
Language	English
Publishing date	2024-02-22
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3932947/v1
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Article ; Online: Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity.

Sergeeva, Alina P / Katsamba, Phinikoula S / Liao, Junzhuo / Sampson, Jared M / Bahna, Fabiana / Mannepalli, Seetha / Morano, Nicholas C / Shapiro, Lawrence / Friesner, Richard A / Honig, Barry

Journal of molecular biology

2023 Volume 435, Issue 15, Page(s) 168187

Abstract	The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used. Overall, we find that FEP performance is superior to that of other computational approaches examined as determined by agreement with experiment and, in particular, by its ability to identify stabilizing mutations. Moreover, the calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in Omicron variants and offer a physical explanation for the underlying mechanism. Overall, our results suggest that despite the significant computational cost, FEP calculations may offer an effective strategy to understand the effects of interfacial mutations on protein-protein binding affinities and, hence, in a variety of practical applications such as the optimization of neutralizing antibodies.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Mutation ; Protein Binding ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Protein Domains
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Language	English
Publishing date	2023-06-22
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.2023.168187
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations.

Sampson, Jared M / Cannon, Daniel A / Duan, Jianxin / Epstein, Jordan C K / Sergeeva, Alina P / Katsamba, Phinikoula S / Mannepalli, Seetha M / Bahna, Fabiana A / Adihou, Hélène / Guéret, Stéphanie M / Gopalakrishnan, Ranganath / Geschwindner, Stefan / Rees, D Gareth / Sigurdardottir, Anna / Wilkinson, Trevor / Dodd, Roger B / De Maria, Leonardo / Mobarec, Juan Carlos / Shapiro, Lawrence /

Honig, Barry / Buchanan, Andrew / Friesner, Richard A / Wang, Lingle

bioRxiv : the preprint server for biology

2024

Abstract: Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in ... ...

Abstract	Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study.
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.22.590325
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules.

Xu, Shuwa / Sergeeva, Alina P / Katsamba, Phinikoula S / Mannepalli, Seetha / Bahna, Fabiana / Bimela, Jude / Zipursky, S Lawrence / Shapiro, Lawrence / Honig, Barry / Zinn, Kai

Cell reports

2022 Volume 39, Issue 1, Page(s) 110618

Abstract: Neurons in the developing brain express many different cell adhesion molecules (CAMs) on their surfaces. CAM-binding affinities can vary by more than 200-fold, but the significance of these variations is unknown. Interactions between the immunoglobulin ... ...

Abstract	Neurons in the developing brain express many different cell adhesion molecules (CAMs) on their surfaces. CAM-binding affinities can vary by more than 200-fold, but the significance of these variations is unknown. Interactions between the immunoglobulin superfamily CAM DIP-α and its binding partners, Dpr10 and Dpr6, control synaptic targeting and survival of Drosophila optic lobe neurons. We design mutations that systematically change interaction affinity and analyze function in vivo. Reducing affinity causes loss-of-function phenotypes whose severity scales with the magnitude of the change. Synaptic targeting is more sensitive to affinity reduction than is cell survival. Increasing affinity rescues neurons that would normally be culled by apoptosis. By manipulating CAM expression together with affinity, we show that the key parameter controlling circuit assembly is surface avidity, which is the strength of adherence between cell surfaces. We conclude that CAM binding affinities and expression levels are finely tuned for function during development.
MeSH term(s)	Animals ; Cell Adhesion ; Cell Adhesion Molecules/genetics ; Cell Adhesion Molecules/metabolism ; Cell Adhesion Molecules, Neuronal/genetics ; Cell Adhesion Molecules, Neuronal/metabolism ; Cell Survival ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; Neurons/metabolism
Chemical Substances	Cell Adhesion Molecules ; Cell Adhesion Molecules, Neuronal ; Drosophila Proteins
Language	English
Publishing date	2022-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110618
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition.

Goodman, Kerry Marie / Katsamba, Phinikoula S / Rubinstein, Rotem / Ahlsén, Göran / Bahna, Fabiana / Mannepalli, Seetha / Dan, Hanbin / Sampogna, Rosemary V / Shapiro, Lawrence / Honig, Barry

eLife

2022 Volume 11

Abstract: The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by ... ...

Abstract	The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by alternating
MeSH term(s)	Cadherins/metabolism ; Cell Communication ; Neurons/metabolism ; Protein Isoforms/metabolism ; Protocadherins
Chemical Substances	Cadherins ; Protein Isoforms ; Protocadherins
Language	English
Publishing date	2022-03-07
Publishing country	England
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.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.72416
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Article: Structural Basis for Accommodation of Emerging B.1.351 and B.1.1.7 Variants by Two Potent SARS-CoV-2 Neutralizing Antibodies.

Cerutti, Gabriele / Rapp, Micah / Guo, Yicheng / Bahna, Fabiana / Bimela, Jude / Reddem, Eswar R / Yu, Jian / Wang, Pengfei / Liu, Lihong / Huang, Yaoxing / Ho, David D / Kwong, Peter D / Sheng, Zizhang / Shapiro, Lawrence

bioRxiv : the preprint server for biology

2021

Abstract: Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical ... ...

Abstract	Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented a response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for both ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies like 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.
Language	English
Publishing date	2021-02-22
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.02.21.432168
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain.

Cerutti, Gabriele / Guo, Yicheng / Wang, Pengfei / Nair, Manoj S / Huang, Yaoxing / Yu, Jian / Liu, Lihong / Katsamba, Phinikoula S / Bahna, Fabiana / Reddem, Eswar R / Kwong, Peter D / Ho, David D / Sheng, Zizhang / Shapiro, Lawrence

bioRxiv : the preprint server for biology

2021

Abstract: Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic ... ...

Abstract	Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here we report the 3.7 Å resolution cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β-sandwich. Interestingly, this pocket has been previously identified as the binding site for hydrophobic molecules including heme metabolites, but we observe their presence to not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains a distinctive neutralization potency with variants of concern (VOC). Overall, we reveal a hydrophobic pocket in NTD proposed for immune evasion can actually be used by the immune system for recognition. Highlights: Cryo-EM structure of neutralizing antibody 5-7 in complex with SARS CoV-2 spike5-7 recognizes NTD outside of the previously identified antigenic supersite5-7 binds to a site known to accommodate numerous hydrophobic ligandsStructural basis of 5-7 neutralization tolerance to some variants of concern.
Language	English
Publishing date	2021-06-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.06.29.450397
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Article ; Online: Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies.

Structure (London, England : 1993)

2021 Volume 29, Issue 7, Page(s) 655–663.e4

Abstract: Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical ... ...

Abstract	Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of the spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented an immune response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies, such as 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/immunology ; Angiotensin-Converting Enzyme 2/metabolism ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/genetics ; Antibodies, Monoclonal/immunology ; Antibodies, Monoclonal/metabolism ; Antibodies, Neutralizing/chemistry ; Antibodies, Neutralizing/genetics ; Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/metabolism ; Antibodies, Viral/chemistry ; Antibodies, Viral/genetics ; Antibodies, Viral/immunology ; Antibodies, Viral/metabolism ; Binding Sites ; Cloning, Molecular ; Cryoelectron Microscopy ; Epitopes/chemistry ; Epitopes/genetics ; Epitopes/immunology ; Epitopes/metabolism ; Gene Expression ; HEK293 Cells ; Humans ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/immunology ; Receptors, Virus/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/immunology ; Recombinant Proteins/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Receptors, Virus ; Recombinant Proteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; 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.2021.05.014
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Free energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity

Sergeeva, Alina P. / Katsamba, Phinikoula S. / Sampson, Jared M. / Bahna, Fabiana / Mannepalli, Seetha / Morano, Nicholas C. / Shapiro, Lawrence / Friesner, Richard A. / Honig, Barry

bioRxiv

Abstract	The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in sequenced samples from infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. We find that FEP performance is significantly better than that of other computational approaches examined here, in part due to its ability to account for protein structure relaxation resulting from the mutation of interfacial residues. Moreover, analysis of FEP trajectories offers physical insights not available from other methods. Notably, FEP calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in the Omicron variant and offer a physical explanation for the underlying mechanism. Our results furthermore suggest a strategy as to how to effectively deploy FEP methods in the optimization of neutralizing antibodies.
Keywords	covid19
Language	English
Publishing date	2022-08-01
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.08.01.502301
Database	COVID19

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