Title: Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

Abstract

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia, is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changesmore » of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.« less

Authors:

Zhao, Zhuoran ^[1]; Shen, Xiayu ^[1]; Chen, Shuang ^[1]; Gu, Jing ^[1]; Wang, Haun ^[1]; Mojica, Maria F.  ^[2];

• Search DOE PAGES for author "Mojica, Maria F."
• Search DOE PAGES for ORCID "0000-0002-1380-9824"

Samanta, Moumita ^[3]; Bhowmik, Debsindhu  ^[4];

• Search DOE PAGES for author "Bhowmik, Debsindhu"
• Search DOE PAGES for ORCID "0000-0001-7770-9091"

Vila, Alejandro J.  ^[5];

• Search DOE PAGES for author "Vila, Alejandro J."
• Search DOE PAGES for ORCID "0000-0002-7978-3233"

Bonomo, Robert A. ^[2]; Haider, Shozeb  ^[1]

• Search DOE PAGES for author "Haider, Shozeb"
• Search DOE PAGES for ORCID "0000-0003-2650-2925"

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+ Show Author Affiliations

1. University College London (United Kingdom)
2. Case Western Reserve University, Cleveland, OH (United States); Department of Veterans Affairs, Cleveland, OH (United States)
3. Georgia Institute of Technology, Atlanta, GA (United States)
4. Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
5. Case Western Reserve University, Cleveland, OH (United States); Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario (Argentina); Universidad Nacional de Rosario (Argentina)

Publication Date:

Fri Feb 24 00:00:00 EST 2023

Research Org.:

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); National Institutes of Health (NIH); Department of Veterans Affairs; USDOE Laboratory Directed Research and Development (LDRD) Program

OSTI Identifier:

1959610

Grant/Contract Number:  

AC05-00OR22725; R01AI100560; BX005307; RO1AI063517

Resource Type:

Accepted Manuscript

Journal Name:

eLife

Additional Journal Information:

Journal Volume: 12; Journal Issue: n/a; Journal ID: ISSN 2050-084X

Publisher:

eLife Sciences Publications, Ltd.

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES