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27 pages, 33404 KiB

Open AccessArticle

Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence

by Paola Ruiz Puentes, Maria C. Henao, Javier Cifuentes, Carolina Muñoz-Camargo, Luis H. Reyes, Juan C. Cruz and Pablo Arbeláez

Membranes 2022, 12(7), 708; https://doi.org/10.3390/membranes12070708 - 14 Jul 2022

Cited by 18 | Viewed by 5243

Abstract

Antibiotic resistance is a worldwide public health problem due to the costs and mortality rates it generates. However, the large pharmaceutical industries have stopped searching for new antibiotics because of their low profitability, given the rapid replacement rates imposed by the increasingly observed [...] Read more.

Antibiotic resistance is a worldwide public health problem due to the costs and mortality rates it generates. However, the large pharmaceutical industries have stopped searching for new antibiotics because of their low profitability, given the rapid replacement rates imposed by the increasingly observed resistance acquired by microorganisms. Alternatively, antimicrobial peptides (AMPs) have emerged as potent molecules with a much lower rate of resistance generation. The discovery of these peptides is carried out through extensive in vitro screenings of either rational or non-rational libraries. These processes are tedious and expensive and generate only a few AMP candidates, most of which fail to show the required activity and physicochemical properties for practical applications. This work proposes implementing an artificial intelligence algorithm to reduce the required experimentation and increase the efficiency of high-activity AMP discovery. Our deep learning (DL) model, called AMPs-Net, outperforms the state-of-the-art method by 8.8% in average precision. Furthermore, it is highly accurate to predict the antibacterial and antiviral capacity of a large number of AMPs. Our search led to identifying two unreported antimicrobial motifs and two novel antimicrobial peptides related to them. Moreover, by coupling DL with molecular dynamics (MD) simulations, we were able to find a multifunctional peptide with promising therapeutic effects. Our work validates our previously proposed pipeline for a more efficient rational discovery of novel AMPs. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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20 pages, 5415 KiB

Open AccessArticle

Translocating Peptides of Biomedical Interest Obtained from the Spike (S) Glycoprotein of the SARS-CoV-2

by Maria C. Henao, Camila Ocasion, Paola Ruiz Puentes, Cristina González-Melo, Valentina Quezada, Javier Cifuentes, Arnovis Yepes, Juan C. Burgos, Juan C. Cruz and Luis H. Reyes

Membranes 2022, 12(6), 600; https://doi.org/10.3390/membranes12060600 - 10 Jun 2022

Cited by 4 | Viewed by 3232

Abstract

At the beginning of 2020, the pandemic caused by the SARS-CoV-2 virus led to the fast sequencing of its genome to facilitate molecular engineering strategies to control the pathogen’s spread. The spike (S) glycoprotein has been identified as the leading therapeutic agent due [...] Read more.

At the beginning of 2020, the pandemic caused by the SARS-CoV-2 virus led to the fast sequencing of its genome to facilitate molecular engineering strategies to control the pathogen’s spread. The spike (S) glycoprotein has been identified as the leading therapeutic agent due to its role in localizing the ACE2 receptor in the host’s pulmonary cell membrane, binding, and eventually infecting the cells. Due to the difficulty of delivering bioactive molecules to the intracellular space, we hypothesized that the S protein could serve as a source of membrane translocating peptides. AHB-1, AHB-2, and AHB-3 peptides were identified and analyzed on a membrane model of DPPC (dipalmitoylphosphatidylcholine) using molecular dynamics (MD) simulations. An umbrella sampling approach was used to quantify the energy barrier necessary to cross the boundary (13.2 to 34.9 kcal/mol), and a flat-bottom pulling helped to gain a deeper understanding of the membrane’s permeation dynamics. Our studies revealed that the novel peptide AHB-1 exhibited comparable penetration potential of already known potent cell-penetrating peptides (CPPs) such as TP2, Buforin II, and Frenatin 2.3s. Results were confirmed by in vitro analysis of the peptides conjugated to chitosan nanoparticles, demonstrating its ability to reach the cytosol and escape endosomes, while maintaining high biocompatibility levels according to standardized assays. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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20 pages, 4866 KiB

Open AccessArticle

iAcety–SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest

by Sharaf Malebary, Shaista Rahman, Omar Barukab, Rehab Ash’ari and Sher Afzal Khan

Membranes 2022, 12(3), 265; https://doi.org/10.3390/membranes12030265 - 25 Feb 2022

Cited by 5 | Viewed by 2076

Abstract

Acetylation is the most important post-translation modification (PTM) in eukaryotes; it has manifold effects on the level of protein that transform an acetyl group from an acetyl coenzyme to a specific site on a polypeptide chain. Acetylation sites play many important roles, including [...] Read more.

Acetylation is the most important post-translation modification (PTM) in eukaryotes; it has manifold effects on the level of protein that transform an acetyl group from an acetyl coenzyme to a specific site on a polypeptide chain. Acetylation sites play many important roles, including regulating membrane protein functions and strongly affecting the membrane interaction of proteins and membrane remodeling. Because of these properties, its correct identification is essential to understand its mechanism in biological systems. As such, some traditional methods, such as mass spectrometry and site-directed mutagenesis, are used, but they are tedious and time-consuming. To overcome such limitations, many computer models are being developed to correctly identify their sequences from non-acetyl sequences, but they have poor efficiency in terms of accuracy, sensitivity, and specificity. This work proposes an efficient and accurate computational model for predicting Acetylation using machine learning approaches. The proposed model achieved an accuracy of 100 percent with the 10-fold cross-validation test based on the Random Forest classifier, along with a feature extraction approach using statistical moments. The model is also validated by the jackknife, self-consistency, and independent test, which achieved an accuracy of 100, 100, and 97, respectively, results far better as compared to the already existing models available in the literature. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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14 pages, 2274 KiB

Open AccessArticle

Structure of ABCB1/P-Glycoprotein in the Presence of the CFTR Potentiator Ivacaftor

by Alessandro Barbieri, Nopnithi Thonghin, Talha Shafi, Stephen M. Prince, Richard F. Collins and Robert C. Ford

Membranes 2021, 11(12), 923; https://doi.org/10.3390/membranes11120923 - 25 Nov 2021

Cited by 16 | Viewed by 3322

Abstract

ABCB1/P-glycoprotein is an ATP binding cassette transporter that is involved in the clearance of xenobiotics, and it affects the disposition of many drugs in the body. Conformational flexibility of the protein within the membrane is an intrinsic part of its mechanism of action, [...] Read more.

ABCB1/P-glycoprotein is an ATP binding cassette transporter that is involved in the clearance of xenobiotics, and it affects the disposition of many drugs in the body. Conformational flexibility of the protein within the membrane is an intrinsic part of its mechanism of action, but this has made structural studies challenging. Here, we have studied different conformations of P-glycoprotein simultaneously in the presence of ivacaftor, a known competitive inhibitor. In order to conduct this, we used high contrast cryo-electron microscopy imaging with a Volta phase plate. We associate the presence of ivacaftor with the appearance of an additional density in one of the conformational states detected. The additional density is in the central aqueous cavity and is associated with a wider separation of the two halves of the transporter in the inward-facing state. Conformational changes to the nucleotide-binding domains are also observed and may help to explain the stimulation of ATPase activity that occurs when transported substrate is bound in many ATP binding cassette transporters. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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14 pages, 2110 KiB

Open AccessEditor’s ChoiceArticle

Cryo-EM Structure of Mechanosensitive Channel YnaI Using SMA2000: Challenges and Opportunities

by Claudio Catalano, Danya Ben-Hail, Weihua Qiu, Paul Blount, Amedee des Georges and Youzhong Guo

Membranes 2021, 11(11), 849; https://doi.org/10.3390/membranes11110849 - 31 Oct 2021

Cited by 9 | Viewed by 3790

Abstract

Mechanosensitive channels respond to mechanical forces exerted on the cell membrane and play vital roles in regulating the chemical equilibrium within cells and their environment. High-resolution structural information is required to understand the gating mechanisms of mechanosensitive channels. Protein-lipid interactions are essential for [...] Read more.

Mechanosensitive channels respond to mechanical forces exerted on the cell membrane and play vital roles in regulating the chemical equilibrium within cells and their environment. High-resolution structural information is required to understand the gating mechanisms of mechanosensitive channels. Protein-lipid interactions are essential for the structural and functional integrity of mechanosensitive channels, but detergents cannot maintain the crucial native lipid environment for purified mechanosensitive channels. Recently, detergent-free systems have emerged as alternatives for membrane protein structural biology. This report shows that while membrane-active polymer, SMA2000, could retain some native cell membrane lipids on the transmembrane domain of the mechanosensitive-like YnaI channel, the complete structure of the transmembrane domain of YnaI was not resolved. This reveals a significant limitation of SMA2000 or similar membrane-active copolymers. This limitation may come from the heterogeneity of the polymers and nonspecific interactions between the polymers and the relatively large hydrophobic pockets within the transmembrane domain of YnaI. However, this limitation offers development opportunities for detergent-free technology for challenging membrane proteins. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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Review

Jump to: Research

21 pages, 3452 KiB

Open AccessReview

Bringing GPCR Structural Biology to Medical Applications: Insights from Both V2 Vasopressin and Mu-Opioid Receptors

by Aurélien Fouillen, Julien Bous, Sébastien Granier, Bernard Mouillac and Remy Sounier

Membranes 2023, 13(6), 606; https://doi.org/10.3390/membranes13060606 - 16 Jun 2023

Cited by 2 | Viewed by 2993

Abstract

G-protein coupled receptors (GPCRs) are versatile signaling proteins that regulate key physiological processes in response to a wide variety of extracellular stimuli. The last decade has seen a revolution in the structural biology of clinically important GPCRs. Indeed, the improvement in molecular and [...] Read more.

G-protein coupled receptors (GPCRs) are versatile signaling proteins that regulate key physiological processes in response to a wide variety of extracellular stimuli. The last decade has seen a revolution in the structural biology of clinically important GPCRs. Indeed, the improvement in molecular and biochemical methods to study GPCRs and their transducer complexes, together with advances in cryo-electron microscopy, NMR development, and progress in molecular dynamic simulations, have led to a better understanding of their regulation by ligands of different efficacy and bias. This has also renewed a great interest in GPCR drug discovery, such as finding biased ligands that can either promote or not promote specific regulations. In this review, we focus on two therapeutically relevant GPCR targets, the V2 vasopressin receptor (V2R) and the mu-opioid receptor (µOR), to shed light on the recent structural biology studies and show the impact of this integrative approach on the determination of new potential clinical effective compounds. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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16 pages, 1573 KiB

Open AccessReview

Insight into the Structure, Functions, and Dynamics of the Leptospira Outer Membrane Proteins with the Pathogenicity

by Shen-Hsing Hsu and Chih-Wei Yang

Membranes 2022, 12(3), 300; https://doi.org/10.3390/membranes12030300 - 7 Mar 2022

Cited by 18 | Viewed by 6657

Abstract

Leptospirosis is a widespread zoonosis that frequently occurs in tropical and subtropical countries. Leptospira enters the host through wounds or mucous membranes and spreads to the whole body through the blood, causing systemic infection. Kidneys are the preferential site where Leptospira accumulates, especially [...] Read more.

Leptospirosis is a widespread zoonosis that frequently occurs in tropical and subtropical countries. Leptospira enters the host through wounds or mucous membranes and spreads to the whole body through the blood, causing systemic infection. Kidneys are the preferential site where Leptospira accumulates, especially in the renal interstitium and renal tubule epithelial cells. Clinical symptoms in humans include high fever, jaundice, renal failure, and severe multiple-organ failure (Weil’s syndrome). Surface-exposed antigens are located at the outermost layer of Leptospira and these potential virulence factors are likely involved in primary host-pathogen interactions, adhesion, and/or invasion. Using the knockout/knockdown techniques to the evaluation of pathogenicity in the virulence factor are the most direct and effective methods and many virulence factors are evaluated including lipopolysaccharides (LPS), Leptospira lipoprotein 32 (LipL32), Leptospira ompA domain protein 22 (Loa22), LipL41, LipL71, Leptospira immunoglobulin-like repeat A (LigA), LigB, and LipL21. In this review, we will discuss the structure, functions, and dynamics of these virulence factors and the roles of these virulence factors in Leptospira pathogenicity. In addition, a protein family with special Leucine-rich repeat (LRR) will also be discussed for their vital role in Leptospira pathogenicity. Finally, these surface-exposed antigens are discussed in the application of the diagnosis target for leptospirosis and compared with the serum microscope agglutination test (MAT), the gold standard for leptospirosis. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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16 pages, 2294 KiB

Open AccessReview

Structures and Dynamics of Dengue Virus Nonstructural Membrane Proteins

by Qingxin Li and Congbao Kang

Membranes 2022, 12(2), 231; https://doi.org/10.3390/membranes12020231 - 17 Feb 2022

Cited by 13 | Viewed by 8853

Abstract

Dengue virus is an important human pathogen threating people, especially in tropical and sub-tropical regions. The viral genome has one open reading frame and encodes one polyprotein which can be processed into structural and nonstructural (NS) proteins. Four of the seven nonstructural proteins, [...] Read more.

Dengue virus is an important human pathogen threating people, especially in tropical and sub-tropical regions. The viral genome has one open reading frame and encodes one polyprotein which can be processed into structural and nonstructural (NS) proteins. Four of the seven nonstructural proteins, NS2A, NS2B, NS4A and NS4B, are membrane proteins. Unlike NS3 or NS5, these proteins do not harbor any enzymatic activities, but they play important roles in viral replication through interactions with viral or host proteins to regulate important pathways and enzymatic activities. The location of these proteins on the cell membrane and the functional roles in viral replication make them important targets for antiviral development. Indeed, NS4B inhibitors exhibit antiviral activities in different assays. Structural studies of these proteins are hindered due to challenges in crystallization and the dynamic nature of these proteins. In this review, the function and membrane topologies of dengue nonstructural membrane proteins are presented. The roles of solution NMR spectroscopy in elucidating the structure and dynamics of these proteins are introduced. The success in the development of NS4B inhibitors proves that this class of proteins is an attractive target for antiviral development. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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31 pages, 3547 KiB

Open AccessReview

New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility

by Robbins Puthenveetil, Eric T. Christenson and Olga Vinogradova

Membranes 2022, 12(2), 227; https://doi.org/10.3390/membranes12020227 - 16 Feb 2022

Cited by 8 | Viewed by 4674

Abstract

A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant [...] Read more.

A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels. Full article

(This article belongs to the Special Issue The Structure, Dynamics and Function of Membrane Proteins)

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