Exploration of HIV-1 fusion peptide–antibody VRC34.01 binding reveals fundamental neutralization sites

Literature Information

Publication Date 2019-08-08
DOI 10.1039/C9CP02909E
Impact Factor 3.676
Authors

Mei Feng, David R. Bell, Hongsuk Kang, Qiwen Shao


View Original

Abstract

Antibody binding to a vulnerable site of HIV envelope glycoprotein (Env), the eight N-terminal residues of the gp41 fusion peptide, renders robust HIV neutralization. Here, we theoretically investigate HIV-1 fusion peptide binding to the neutralizing antibody N123–VRC34.01. We explore numerous fusion peptide mutations using all-atom molecular dynamics simulation with explicit-solvent models. Simulation results show that the hydrophobic interaction between Ile515 in the HIV-1 fusion peptide and the antibody VRC34.01 Fab plays an important role in antibody binding. Furthermore, we verify by free energy perturbation (FEP) calculations that two point mutations of Ile515Thr or Ile515Ala can dramatically weaken the binding affinity. Our findings provide new insights into fusion peptide–VRC34.01 binding, which can ultimately be utilized to design effective HIV vaccines.

Related Literature

Mechanism of activated chemiluminescence of cyclic peroxides: 1,2-dioxetanes and 1,2-dioxetanones

Ignacio Fdez. Galván, Daniel Roca-Sanjuán, Erick L. Bastos, Wilhelm J. Baader, Roland Lindh

2017-01-03 Paper

DOI: 10.1039/C6CP08154A

Modeling the abnormally slow infiltration rate in mesoporous films

Claudio L. A. Berli, Magalí Mercuri, Martín G. Bellino

2016-12-12 Communication

DOI: 10.1039/C6CP06602J

Temperature-dependent ESR and computational studies on antiferromagnetic electron transfer in the yeast NADH dehydrogenase Ndi1

Kaiqi Wu, Wenfei Li, Lu Yu, Wei Tong, Yue Feng, Shenglong Ling, Longhua Zhang, Xiao Zheng, Maojun Yang

2017-01-09 Paper

DOI: 10.1039/C6CP08107J

Back cover

Cover

DOI: 10.1039/C7CP90026K

Comparative study of the intermolecular dynamics of imidazolium-based ionic liquids with linear and branched alkyl chains: OHD-RIKES measurements

Lianjie Xue, Fehmi Bardak, George Tamas, Edward L. Quitevis

2017-01-19 Paper

DOI: 10.1039/C6CP08263G

Room-temperature ferromagnetism in the two-dimensional layered Cu2MoS4 nanosheets

Ke Zhang, Rashid Khan, Hongyan Guo, Irfan Ali, Xiuling Li, Yunxiang Lin, Haiping Chen, Wensheng Yan, Xiaojun Wu, Li Song

2016-12-12 Communication

DOI: 10.1039/C6CP07270D

A cationic naphthyl derivative defies the non-equilibrated excited rotamers principle

A. Cesaretti, B. Carlotti, F. Elisei, C. G. Fortuna, G. Consiglio, A. Spalletti

2017-01-16 Paper

DOI: 10.1039/C6CP08311K

You might also like

Compound Q&A

What precautions should be taken when handling 4-(2-Furylmethyl)thiomorpholine 1,1-dioxide (CAS: 79206-94-3)?

When handling 4-(2-Furylmethyl)thiomorpholine 1,1-dioxide (CAS: 79206-94-3), it ...

79206-94-34-(2-Furylmethyl)thi...
Compound Q&A

What precautions should be taken when handling 4-Chloro-N-[2-(4-morpholinyl)ethyl]benzamide (CAS: 71320-77-9)?

When handling 4-Chloro-N-[2-(4-morpholinyl)ethyl]benzamide (CAS: 71320-77-9), it...

71320-77-94-Chloro-N-[2-(4-mor...
Compound Q&A

How should waste containing 2-[2-(2-Methoxyethoxy)ethoxy]ethyl 4-methylbenzenesulfonate (CAS: 62921-74-8) be handled?

Waste containing this compound (CAS: 62921-74-8) should be handled according to ...

62921-74-82-[2-(2-Methoxyethox...
Compound Q&A

How should waste containing (S)-Methyl 2-amino-3-cyclohexylpropanoate be handled?

Waste containing (S)-Methyl 2-amino-3-cyclohexylpropanoate should be collected i...

40056-18-6(S)-Methyl 2-amino-3...
166882-70-85-({4-[(2S,4R)-4-Hyd...
Compound Q&A

Are there alternatives to (2E)-3-(3,4-Dichlorophenyl)acrylic acid (CAS: 7312-27-8) in synthesis?

There are several alternatives to (2E)-3-(3,4-Dichlorophenyl)acrylic acid in syn...

7312-27-8(2E)-3-(3,4-Dichloro...
Compound Q&A

How should Ethyl 6-(2-nitrophenyl)imidazo[2,1-b][1,3]thiazole-3-carboxylate (CAS: 925437-84-9) be stored?

Ethyl 6-(2-nitrophenyl)imidazo[2,1-b][1,3]thiazole-3-carboxylate (CAS: 925437-84...

925437-84-9Ethyl 6-(2-nitrophen...
Compound Q&A

How should waste containing 2-(1,3-Thiazol-2-yl)ethanamine (CAS: 18453-07-1) be handled?

Waste containing 2-(1,3-Thiazol-2-yl)ethanamine (CAS: 18453-07-1) should be coll...

18453-07-12-(1,3-Thiazol-2-yl)...
Compound Q&A

How is Methyl 5-iodo-2-methylbenzoate (CAS: 103440-54-6) typically synthesized?

Methyl 5-iodo-2-methylbenzoate can be synthesized through the iodination of meth...

103440-54-6Methyl 5-iodo-2-meth...
Compound Q&A

How is 5-Chloro[1,2,4]triazolo[1,5-a]pyridine (CAS: 1427399-34-5) typically synthesized?

5-Chloro[1,2,4]triazolo[1,5-a]pyridine is commonly synthesized via the condensat...

1427399-34-55-Chloro[1,2,4]triaz...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.