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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 30842

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Dr. Istvan Simon

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1. Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
2. Center of Excellence of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
Interests: protein structures; protein dynamics; protein conformation; protein folding; protein bioinformatics; protein interactions; membrane proteins; protein stability; intrinsically disordered proteins; protein biophysics; protein binding; molecular biophysics; protein refolding; membrane transport proteins; computational structural biology; structural bioinformatics
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Dr. Csaba Magyar

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Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
Interests: protein bioinformatics; protein stability; intrinsically disordered proteins; protein structure; protein structure modeling; protein dynamics; molecular dynamics simulation; protein conformation; computational structural biology; structural bioinformatics; drug design; structure based drug design
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Special Issue Information

Dear Colleagues,

In recent years, new frontiers have opened up in protein structure research. Besides the traditional forms of proteins, such as folded water-soluble proteins, transmembrane- and membrane-associated proteins, and disordered proteins which are able to fold on the surface of folded proteins or other stable macromolecules, new forms of proteins and protein complexes have emerged. Among others, fuzzy complexes in which, during physiological function, at least one protein component is still in disordered form; and mutual synergistic folding complexes, in which two or more disordered proteins help each other to fold, are new subclasses of proteins. Combinations of the above-mentioned proteins, such as partially disordered proteins or proteins participating in liquid–liquid phase separation, represent new forms of proteins. These all encompass new and interesting fields of protein structure research.

As the guest editors of this Special Issue of IJMS titled “Protein Structure Research”, we would like to invite you to contribute a paper related to protein structures.

Prof. Dr. Istvan Simon
Dr. Csaba Magyar
Guest Editors

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Keywords

fuzzy complexes
intrinsically disordered proteins
liquid-liquid phase separation
mutual synergistic folding
protein folding
protein structure
protein-protein interactions
transmembrane proteins

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Published Papers (11 papers)

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Research

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9 pages, 1123 KiB

Open AccessCommunication

The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method

by Miklós Cserző, Birgit Eisenhaber, Frank Eisenhaber, Csaba Magyar and István Simon

Int. J. Mol. Sci. 2023, 24(18), 14016; https://doi.org/10.3390/ijms241814016 - 13 Sep 2023

Cited by 1 | Viewed by 1258 | Correction

Abstract

The dense alignment surface (DAS) transmembrane (TM) prediction method was first published more than 25 years ago. DAS was the one of the earliest tools to discriminate TM proteins from globular ones and to predict the sequence positions of TM helices in proteins with high accuracy from their amino acid sequence alone. The algorithmic improvements that followed in 2002 (DAS-TMfilter) made it one of the best performing tools among those relying on local sequence information for TM prediction. Since then, many more experimental data about membrane proteins (including thousands of 3D structures of membrane proteins) have accumulated but there has been no significant improvement concerning performance in the area of TM helix prediction tools. Here, we report a new implementation of the DAS-TMfilter prediction web server. We reevaluated the performance of the method using a five-times-larger, updated test dataset. We found that the method performs at essentially the same accuracy as the original even without any change to the parametrization of the program despite the much larger dataset. Thus, the approach captures the physico-chemistry of TM helices well, essentially solving this scientific problem. Full article

(This article belongs to the Special Issue Protein Structure Research)

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11 pages, 2872 KiB

Open AccessArticle

Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding

by Tej Sharma, Bernard Gerstman and Prem Chapagain

Int. J. Mol. Sci. 2023, 24(16), 12586; https://doi.org/10.3390/ijms241612586 - 9 Aug 2023

Cited by 6 | Viewed by 2047

Abstract

The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein’s receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD–ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants’ fitness over their predecessors. Full article

(This article belongs to the Special Issue Protein Structure Research)

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15 pages, 9415 KiB

Open AccessArticle

Investigation of Molecular Interactions Mechanism of Pembrolizumab and PD-1

by Simiao Wang and Faez Iqbal Khan

Int. J. Mol. Sci. 2023, 24(13), 10684; https://doi.org/10.3390/ijms241310684 - 26 Jun 2023

Cited by 8 | Viewed by 5298

Abstract

Human programmed cell death protein 1 (PD-1) is a checkpoint protein involved in the regulation of immune response. Antibodies are widely used as inhibitors that block the immune checkpoint, preventing strong immune responses. Pembrolizumab is an FDA-approved IgG4 antibody with PD-1 inhibitory ability for the treatment of melanoma. In this study, we investigated the effect of Pembrolizumab on the conformational changes in PD-1 using extensive molecular modeling and simulation approaches. Our study revealed that during the 200 ns simulation, the average values of the solvent accessible surface area, the radius of gyration, and internal hydrogen bonds of PD-1 were 64.46 nm², 1.38 nm and 78, respectively, while these values of PD-1 in the PD-1/Pembrolizumab complex were 67.29 nm², 1.39 nm and 76, respectively. The RMSD value of PD-1 gradually increased until 80 ns and maintained its stable conformation at 0.32 nm after 80 ns, while this value of PD-1 in the PD-1/Pembrolizumab complex maintained an increasing trend during 200 ns. The interaction between PD-1 and Pembrolizumab led to a flexible but stable structure of PD-1. PD-1 rotated around the rotation axis of the C’D loop and gradually approached Pembrolizumab. The number of hydrogen bonds involved in the interactions on the C and C’ strands increased from 4 at 100 ns to 7 at 200 ns. The strong affinity of Pembrolizumab for the C’D and FG loops of PD-1 disrupted the interactions between PD-1 and PD-L1. Inhibition of the interaction between PD-1 and PD-L1 increased the T cell activity, and is effective in controlling and curing cancer. Further experimental work can be performed to support this finding. Full article

(This article belongs to the Special Issue Protein Structure Research)

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18 pages, 4404 KiB

Open AccessArticle

Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy

by Arina I. Gordeeva, Anastasia A. Valueva, Maria O. Ershova, Elizaveta E. Rybakova, Ivan D. Shumov, Andrey F. Kozlov, Vadim S. Ziborov, Maria G. Zavialova, Victor G. Zgoda, Yuri D. Ivanov, Alexander I. Archakov and Tatyana O. Pleshakova

Int. J. Mol. Sci. 2023, 24(10), 8999; https://doi.org/10.3390/ijms24108999 - 19 May 2023

Cited by 1 | Viewed by 2192

Abstract

Mass spectrometry (MS) is one of the main techniques for protein identification. Herein, MS has been employed for the identification of bovine serum albumin (BSA), which was covalently immobilized on the surface of a mica chip intended for investigation by atomic force microscopy (AFM). For the immobilization, two different types of crosslinkers have been used: 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) and dithiobis(succinimidyl propionate) (DSP). According to the data obtained by using an AFM-based molecular detector, the SuccBB crosslinker was more efficient in BSA immobilization than the DSP. The type of crosslinker used for protein capturing has been found to affect the results of MS identification. The results obtained herein can be applied in the development of novel systems intended for the highly sensitive analysis of proteins with molecular detectors. Full article

(This article belongs to the Special Issue Protein Structure Research)

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14 pages, 3884 KiB

Open AccessArticle

Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus

by Yan Qin, Yuqiao Zhou, Yinghua Cao, Yanpeng Ren, Pujuan Deng, Junyi Jiang and Zhanxin Wang

Int. J. Mol. Sci. 2023, 24(10), 8730; https://doi.org/10.3390/ijms24108730 - 13 May 2023

Viewed by 1743

Abstract

The multicomponent polymerase associated factor 1 (Paf1) complex (PAF1C) is an important transcription elongation factor that upregulates RNA polymerase II-mediated genome-wide transcription. PAF1C can regulate transcription through direct association with the polymerase or by impacting the chromatin structure epigenetically. In recent years, significant progress has been made in understanding the molecular mechanisms of PAF1C. However, high-resolution structures that can clarify the interaction details among the components of the complex are still needed. In this study, we evaluated the structural core of the yeast PAF1C containing the four components Ctr9, Paf1, Cdc73 and Rtf1 at high resolution. We observed the interaction details among these components. In particular, we identified a new binding surface of Rtf1 on PAF1C and found that the C-terminal sequence of Rtf1 dramatically changed during evolution, which may account for its different binding affinities to PAF1C among species. Our work presents a precise model of PAF1C, which will facilitate our understanding of the molecular mechanism and the in vivo function of the yeast PAF1C. Full article

(This article belongs to the Special Issue Protein Structure Research)

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21 pages, 4599 KiB

Open AccessArticle

Structural Characterization of Neisseria gonorrhoeae Bacterial Peroxidase—Insights into the Catalytic Cycle of Bacterial Peroxidases

by Cláudia S. Nóbrega, Ana Luísa Carvalho, Maria João Romão and Sofia R. Pauleta

Int. J. Mol. Sci. 2023, 24(7), 6246; https://doi.org/10.3390/ijms24076246 - 26 Mar 2023

Cited by 3 | Viewed by 2505

Abstract

Neisseria gonorrhoeae is an obligate human pathogenic bacterium responsible for gonorrhea, a sexually transmitted disease. The bacterial peroxidase, an enzyme present in the periplasm of this bacterium, detoxifies the cells against hydrogen peroxide and constitutes one of the primary defenses against exogenous and endogenous oxidative stress in this organism. The 38 kDa heterologously produced bacterial peroxidase was crystallized in the mixed-valence state, the active state, at pH 6.0, and the crystals were soaked with azide, producing the first azide-inhibited structure of this family of enzymes. The enzyme binds exogenous ligands such as cyanide and azide, which also inhibit the catalytic activity by coordinating the P heme iron, the active site, and competing with its substrate, hydrogen peroxide. The inhibition constants were estimated to be 0.4 ± 0.1 µM and 41 ± 5 mM for cyanide and azide, respectively. Imidazole also binds and inhibits the enzyme in a more complex mechanism by binding to P and E hemes, which changes the reduction potential of the latest heme. Based on the structures now reported, the catalytic cycle of bacterial peroxidases is revisited. The inhibition studies and the crystal structure of the inhibited enzyme comprise the first platform to search and develop inhibitors that target this enzyme as a possible new strategy against N. gonorrhoeae. Full article

(This article belongs to the Special Issue Protein Structure Research)

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14 pages, 4505 KiB

Open AccessArticle

Structural Investigation of Diclofenac Binding to Ovine, Caprine, and Leporine Serum Albumins

by Julita A. Talaj, Kamil Zielinski and Anna Bujacz

Int. J. Mol. Sci. 2023, 24(2), 1534; https://doi.org/10.3390/ijms24021534 - 12 Jan 2023

Cited by 2 | Viewed by 2607

Abstract

Free drug concentration in the blood sera is crucial for its appropriate activity. Serum albumin, the universal blood carrier protein, is responsible for transporting drugs and releasing them into the bloodstream. Therefore, a drug’s binding to SA is especially important for its bioavailability and it is a key problem in the drug design process. In this paper, we present crystal structures of three animal serum albumin complexes: ovine, caprine, and leporine, with diclofenac, a popular non-steroidal anti-inflammatory drug that is used in therapy of chronic and acute pain. Details of diclofenac binding mode by the presented serum albumins are compared with analogous complexes of human and equine serum albumins. The analysis of the occupied binding pockets in crystal structures of the investigated serum albumins from different mammals shows that they have two common and a number of unique diclofenac binding sites. The most intriguing is the fact that the albumins from the described species are able to bind different numbers of molecules of this popular anti-inflammatory drug, but none of the binding sites overlap with ones in the human serum albumin. Full article

(This article belongs to the Special Issue Protein Structure Research)

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14 pages, 2611 KiB

Open AccessArticle

Modelling the Transitioning of SARS-CoV-2 nsp3 and nsp4 Lumenal Regions towards a More Stable State on Complex Formation

by Nele Klatte, Denis C. Shields and Clement Agoni

Int. J. Mol. Sci. 2023, 24(1), 720; https://doi.org/10.3390/ijms24010720 - 31 Dec 2022

Cited by 7 | Viewed by 3668

Abstract

During coronavirus infection, three non-structural proteins, nsp3, nsp4, and nsp6, are of great importance as they induce the formation of double-membrane vesicles where the replication and transcription of viral gRNA takes place, and the interaction of nsp3 and nsp4 lumenal regions triggers membrane pairing. However, their structural states are not well-understood. We investigated the interactions between nsp3 and nsp4 by predicting the structures of their lumenal regions individually and in complex using AlphaFold2 as implemented in ColabFold. The ColabFold prediction accuracy of the nsp3–nsp4 complex was increased compared to nsp3 alone and nsp4 alone. All cysteine residues in both lumenal regions were modelled to be involved in intramolecular disulphide bonds. A linker region in the nsp4 lumenal region emerged as crucial for the interaction, transitioning to a structured state when predicted in complex. The key interactions modelled between nsp3 and nsp4 appeared stable when the transmembrane regions of nsp3 and nsp4 were added to the modelling either alone or together. While molecular dynamics simulations (MD) demonstrated that the proposed model of the nsp3 lumenal region on its own is not stable, key interactions between nsp and nsp4 in the proposed complex model appeared stable after MD. Together, these observations suggest that the interaction is robust to different modelling conditions. Understanding the functional importance of the nsp4 linker region may have implications for the targeting of double membrane vesicle formation in controlling coronavirus infection. Full article

(This article belongs to the Special Issue Protein Structure Research)

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20 pages, 1997 KiB

Open AccessArticle

Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor

by Sergey E. Kruchinin, Ekaterina E. Kislinskaya, Gennady N. Chuev and Marina V. Fedotova

Int. J. Mol. Sci. 2022, 23(23), 14785; https://doi.org/10.3390/ijms232314785 - 26 Nov 2022

Cited by 6 | Viewed by 1924

Abstract

Characterization of the hydrated state of a protein is crucial for understanding its structural stability and function. In the present study, we have investigated the 3D hydration structure of the protein BPTI (bovine pancreatic trypsin inhibitor) by molecular dynamics (MD) and the integral equation method in the three-dimensional reference interaction site model (3D-RISM) approach. Both methods have found a well-defined hydration layer around the protein and revealed the localization of BPTI buried water molecules corresponding to the X-ray crystallography data. Moreover, under 3D-RISM calculations, the obtained positions of waters bound firmly to the BPTI sites are in reasonable agreement with the experimental results mentioned above for the BPTI crystal form. The analysis of the 3D hydration structure (thickness of hydration shell and hydration numbers) was performed for the entire protein and its polar and non-polar parts using various cut-off distances taken from the literature as well as by a straightforward procedure proposed here for determining the thickness of the hydration layer. Using the thickness of the hydration shell from this procedure allows for calculating the total hydration number of biomolecules properly under both methods. Following this approach, we have obtained the thickness of the BPTI hydration layer of 3.6 Å with 369 water molecules in the case of MD simulation and 3.9 Å with 333 water molecules in the case of the 3D-RISM approach. The above procedure was also applied for a more detailed description of the BPTI hydration structure near the polar charged and uncharged radicals as well as non-polar radicals. The results presented for the BPTI as an example bring new knowledge to the understanding of protein hydration. Full article

(This article belongs to the Special Issue Protein Structure Research)

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20 pages, 3366 KiB

Open AccessArticle

Staphylococcus aureus Exfoliative Toxin E, Oligomeric State and Flip of P186: Implications for Its Action Mechanism

by Carolina Gismene, Jorge Enrique Hernández González, Angela Rocio Niño Santisteban, Andrey Fabricio Ziem Nascimento, Lucas dos Santos Cunha, Fábio Rogério de Moraes, Cristiano Luis Pinto de Oliveira, Caio C. Oliveira, Paola Jocelan Scarin Provazzi, Pedro Geraldo Pascutti, Raghuvir Krishnaswamy Arni and Ricardo Barros Mariutti

Int. J. Mol. Sci. 2022, 23(17), 9857; https://doi.org/10.3390/ijms23179857 - 30 Aug 2022

Cited by 4 | Viewed by 2657

Abstract

Staphylococcal exfoliative toxins (ETs) are glutamyl endopeptidases that specifically cleave the Glu381-Gly382 bond in the ectodomains of desmoglein 1 (Dsg1) via complex action mechanisms. To date, four ETs have been identified in different Staphylococcus aureus strains and ETE is the most recently characterized. The unusual properties of ETs have been attributed to a unique structural feature, i.e., the 180° flip of the carbonyl oxygen (O) of the nonconserved residue 192/186 (ETA/ETE numbering), not conducive to the oxyanion hole formation. We report the crystal structure of ETE determined at 1.61 Å resolution, in which P186(O) adopts two conformations displaying a 180° rotation. This finding, together with free energy calculations, supports the existence of a dynamic transition between the conformations under the tested conditions. Moreover, enzymatic assays showed no significant differences in the esterolytic efficiency of ETE and ETE/P186G, a mutant predicted to possess a functional oxyanion hole, thus downplaying the influence of the flip on the activity. Finally, we observed the formation of ETE homodimers in solution and the predicted homodimeric structure revealed the participation of a characteristic nonconserved loop in the interface and the partial occlusion of the protein active site, suggesting that monomerization is required for enzymatic activity. Full article

(This article belongs to the Special Issue Protein Structure Research)

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Review

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Open AccessReview

Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody

by Myeongsang Lee, Marian Major and Huixiao Hong

Int. J. Mol. Sci. 2023, 24(4), 3774; https://doi.org/10.3390/ijms24043774 - 14 Feb 2023

Cited by 6 | Viewed by 2726

Abstract

Since November 2021, Omicron has been the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that causes the coronavirus disease 2019 (COVID-19) and has continuously impacted human health. Omicron sublineages are still increasing and cause increased transmission and infection rates. The additional 15 mutations on the receptor binding domain (RBD) of Omicron spike proteins change the protein conformation, enabling the Omicron variant to evade neutralizing antibodies. For this reason, many efforts have been made to design new antigenic variants to induce effective antibodies in SARS-CoV-2 vaccine development. However, understanding the different states of Omicron spike proteins with and without external molecules has not yet been addressed. In this review, we analyze the structures of the spike protein in the presence and absence of angiotensin-converting enzyme 2 (ACE2) and antibodies. Compared to previously determined structures for the wildtype spike protein and other variants such as alpha, beta, delta, and gamma, the Omicron spike protein adopts a partially open form. The open-form spike protein with one RBD up is dominant, followed by the open-form spike protein with two RBD up, and the closed-form spike protein with the RBD down. It is suggested that the competition between antibodies and ACE2 induces interactions between adjacent RBDs of the spike protein, which lead to a partially open form of the Omicron spike protein. The comprehensive structural information of Omicron spike proteins could be helpful for the efficient design of vaccines against the Omicron variant. Full article

(This article belongs to the Special Issue Protein Structure Research)

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