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Vasconcelos AA, Estrada JC, Caruso IP, Kurtenbach E, Zingali RB, Almeida FCL. Toward the mechanism of jarastatin (rJast) inhibition of the integrin αVβ3. Int J Biol Macromol 2024; 255:128078. [PMID: 37972836 DOI: 10.1016/j.ijbiomac.2023.128078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/04/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Disintegrins are a family of cysteine-rich small proteins that were first identified in snake venom. The high divergence of disintegrins gave rise to a plethora of functions, all related to the interaction with integrins. Disintegrins evolved to interact selectively with different integrins, eliciting many physiological outcomes and being promising candidates for the therapy of many pathologies. We used NMR to determine the structure and dynamics of the recombinant disintegrin jarastatin (rJast) and its interaction with the cancer-related integrin αVβ3. rJast displayed the canonical fold of a medium-sized disintegrin and showed complex dynamic in multiple timescales. We used NMR experiments to map the interaction of rJast with αVβ3, and molecular docking followed by molecular dynamics (MD) simulation to describe the first structural model of a disintegrin/integrin complex. We showed that not only the RGD loop participates in the interaction, but also the N-terminal domain. rJast plasticity was essential for the interaction with αVβ3 and correlated with the main modes of motion depicted in the MD trajectories. In summary, our study provides novel structural insights that enhance our comprehension of the mechanisms underlying disintegrin functionality.
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Affiliation(s)
- Ariana A Vasconcelos
- Laboratório de RMN de Biomoléculas, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge C Estrada
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Icaro P Caruso
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto, São Paulo, Brazil
| | - Eleonora Kurtenbach
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B Zingali
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fabio C L Almeida
- Laboratório de RMN de Biomoléculas, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro Nacional de Ressonância Magnética Nuclear (CNRMN), Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Mohid SA, Biswas K, Won T, Mallela LS, Gucchait A, Butzke L, Sarkar R, Barkham T, Reif B, Leipold E, Roy S, Misra AK, Lakshminarayanan R, Lee D, Bhunia A. Structural insights into the interaction of antifungal peptides and ergosterol containing fungal membrane. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183996. [PMID: 35753394 DOI: 10.1016/j.bbamem.2022.183996] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
The treatment of invasive drug-resistant and potentially life-threatening fungal infections is limited to few therapeutic options that are usually associated with severe side effects. The development of new effective antimycotics with a more tolerable side effect profile is therefore of utmost clinical importance. Here, we used a combination of complementary in vitro assays and structural analytical methods to analyze the interaction of the de novo antimicrobial peptide VG16KRKP with the sterol moieties of biological cell membranes. We demonstrate that VG16KRKP disturbs the structural integrity of fungal membranes both invitro and in model membrane system containing ergosterol along with phosphatidylethanolamine lipid and exhibits broad-spectrum antifungal activity. As revealed by systematic structure-function analysis of mutated VG16KRKP analogs, a specific pattern of basic and hydrophobic amino acid side chains in the primary peptide sequence determines the selectivity of VG16KRKP for fungal specific membranes.
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Affiliation(s)
- Sk Abdul Mohid
- Department of Biophysics, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Sector V, Kolkata 700091, India
| | - Karishma Biswas
- Department of Biophysics, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Sector V, Kolkata 700091, India
| | - TaeJun Won
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Lakshmi S Mallela
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India
| | - Arin Gucchait
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Sector V, Kolkata 700091, India
| | - Lena Butzke
- Department of Anesthesiology and Intensive Care & Center of Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | | | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore
| | - Bernd Reif
- Technical University of Munich, 85748 Garching, Germany
| | - Enrico Leipold
- Department of Anesthesiology and Intensive Care & Center of Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Sanhita Roy
- Prof. Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500034, India
| | - Anup K Misra
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Sector V, Kolkata 700091, India
| | | | - DongKuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea.
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Sector V, Kolkata 700091, India.
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Zhou GP, Liao SM, Chen D, Huang RB. The Cooperative Effect between Polybasic Region (PBR) and Polysialyltransferase Domain (PSTD) within Tumor-Target Polysialyltranseferase ST8Sia II. Curr Top Med Chem 2020; 19:2831-2841. [PMID: 31755393 DOI: 10.2174/1568026619666191121145924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 12/29/2022]
Abstract
ST8Sia II (STX) is a highly homologous mammalian polysialyltransferase (polyST), which is a validated tumor-target in the treatment of cancer metastasis reliant on tumor cell polysialylation. PolyST catalyzes the synthesis of α2,8-polysialic acid (polySia) glycans by carrying out the activated CMP-Neu5Ac (Sia) to N- and O-linked oligosaccharide chains on acceptor glycoproteins. In this review article, we summarized the recent studies about intrinsic correlation of two polybasic domains, Polysialyltransferase domain (PSTD) and Polybasic region (PBR) within ST8Sia II molecule, and suggested that the critical amino acid residues within the PSTD and PBR motifs of ST8Sia II for polysialylation of Neural cell adhesion molecules (NCAM) are related to ST8Sia II activity. In addition, the conformational changes of the PSTD domain due to point mutations in the PBR or PSTD domain verified an intramolecular interaction between the PBR and the PSTD. These findings have been incorporated into Zhou's NCAM polysialylation/cell migration model, which will provide new perspectives on drug research and development related to the tumor-target ST8Sia II.
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Affiliation(s)
- Guo-Ping Zhou
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,Gordon Life Science Institute, NC 27804, United States
| | - Si-Ming Liao
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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Deng L, Kitova EN, Klassen JS. Dissociation kinetics of the streptavidin-biotin interaction measured using direct electrospray ionization mass spectrometry analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:49-56. [PMID: 23247970 DOI: 10.1007/s13361-012-0533-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Dissociation rate constants (k (off)) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S(4)) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S(4) + 4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S(4) + iB) species. The two methods were found to yield k (off) values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin-streptavidin interaction in solution were established from the k (off) values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal mol(-1), with the reported value. In addition to providing a quantitative measure of k (off), the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S(4) + iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S(4) occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.
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Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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