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Journal articles on the topic 'Structural alignment of biomolecular proteins'

Author: Grafiati

Published: 19 February 2023

Last updated: 20 February 2023

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1

Wang, Jiyao, Philippe Youkharibache, Dachuan Zhang, et al. "iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures." Bioinformatics 36, no. 1 (2019): 131–35. http://dx.doi.org/10.1093/bioinformatics/btz502.

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Abstract Motivation Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. Results iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/anno

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Prestegard, J. H., H. M. Al-Hashimi, and J. R. Tolman. "NMR structures of biomolecules using field oriented media and residual dipolar couplings." Quarterly Reviews of Biophysics 33, no. 4 (2000): 371–424. http://dx.doi.org/10.1017/s0033583500003656.

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1. Introduction 3721.1 Residual dipolar couplings as a route to structure and dynamics 3721.2 A brief history of oriented phase high resolution NMR 3742. Theoretical treatment of dipolar interactions 3762.1 Anisotropic interactions as probes of macromolecular structure and dynamics 3762.1.1 The dipolar interaction 3762.1.2 Averaging in the solution state 3772.2 Ordering of a rigid body 3772.2.1 The Saupe order tensor 3782.2.2 Orientational probability distribution function 3802.2.3 The generalized degree of order 3802.3 Molecular structure and internal dynamics 3813. Inducing molecular order i

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Hou, Qingzhen, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, and K. Anton Feenstra. "SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions." Bioinformatics 35, no. 22 (2019): 4794–96. http://dx.doi.org/10.1093/bioinformatics/btz428.

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Abstract Motivation Interpretation of ubiquitous protein sequence data has become a bottleneck in biomolecular research, due to a lack of structural and other experimental annotation data for these proteins. Prediction of protein interaction sites from sequence may be a viable substitute. We therefore recently developed a sequence-based random forest method for protein–protein interface prediction, which yielded a significantly increased performance than other methods on both homomeric and heteromeric protein–protein interactions. Here, we present a webserver that implements this method effici

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Bax, Ad, and Alexander Grishaev. "Weak alignment NMR: a hawk-eyed view of biomolecular structure." Current Opinion in Structural Biology 15, no. 5 (2005): 563–70. http://dx.doi.org/10.1016/j.sbi.2005.08.006.

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5

Azginoglu, Nuh, Zafer Aydin, and Mete Celik. "Structural profile matrices for predicting structural properties of proteins." Journal of Bioinformatics and Computational Biology 18, no. 04 (2020): 2050022. http://dx.doi.org/10.1142/s0219720020500225.

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Predicting structural properties of proteins plays a key role in predicting the 3D structure of proteins. In this study, new structural profile matrices (SPM) are developed for protein secondary structure, solvent accessibility and torsion angle class predictions, which could be used as input to 3D prediction algorithms. The structural templates employed in computing SPMs are detected by eight alignment methods in LOMETS server, gap affine alignment method, ScanProsite, PfamScan, and HHblits. The contribution of each template is weighted by its similarity to target, which is assessed by severa

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Dhar, Sunandan, Vishesh Sood, Garima Lohiya, Harini Deivendran, and Dhirendra S. Katti. "Role of Physicochemical Properties of Protein in Modulating the Nanoparticle-Bio Interface." Journal of Biomedical Nanotechnology 16, no. 8 (2020): 1276–95. http://dx.doi.org/10.1166/jbn.2020.2958.

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Nanoparticles, on exposure to the biological milieu, tend to interact with macromolecules to form a biomolecular corona. The biomolecular corona confers a unique biological identity to nanoparticles, and its protein composition plays a deterministic role in the biological fate of nanoparticles. The physiological behavior of proteins stems from their physicochemical properties, including surface charge, hydrophobicity, and structural stability. However, there is insufficient understanding about the role of physicochemical properties of proteins in biomolecular corona formation. We hypothesized

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Radusky, Leandro G., and Luis Serrano. "pyFoldX: enabling biomolecular analysis and engineering along structural ensembles." Bioinformatics 38, no. 8 (2022): 2353–55. http://dx.doi.org/10.1093/bioinformatics/btac072.

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Abstract Summary Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software has proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modelling software.

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8

Moreau, David W., Hakan Atakisi, and Robert E. Thorne. "Ice in biomolecular cryocrystallography." Acta Crystallographica Section D Structural Biology 77, no. 4 (2021): 540–54. http://dx.doi.org/10.1107/s2059798321001170.

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Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729–727], a revised metric is defined for detecting ice from deposited protein structure-factor dat

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Cuthbertson, Jonathan, and Mark S. P. Sansom. "Structural bioinformatics and molecular simulations: Looking at membrane proteins." Biochemist 26, no. 4 (2004): 25–28. http://dx.doi.org/10.1042/bio02604025.

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Membrane proteins account for approximately 25% of all genes, and constitute approximately 50% of potential drug targets. The steady increase in the number of three-dimensional structures for membrane proteins means that the twin disciplines of structural bioinformatics and biomolecular simulations may be applied to this important class of molecules. Bioinformatics studies are starting to reveal, for example, sequence motifs that govern how transmembrane -helices pack together. Simulations are revealing the dynamic behaviour of membrane proteins and the nature of their often transient interact

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Shillcock, J. C., M. Brochut, E. Chénais, and J. H. Ipsen. "Phase behaviour and structure of a model biomolecular condensate." Soft Matter 16, no. 27 (2020): 6413–23. http://dx.doi.org/10.1039/d0sm00813c.

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11

Scholl, Daniel, and Ashok A. Deniz. "Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates." Journal of Molecular Biology 434, no. 1 (2022): 167348. http://dx.doi.org/10.1016/j.jmb.2021.167348.

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Terlecki-Zaniewicz, Stefan, Theresa Humer, Thomas Eder, et al. "Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression." Nature Structural & Molecular Biology 28, no. 2 (2021): 190–201. http://dx.doi.org/10.1038/s41594-020-00550-w.

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George, Deepu K., Rohit Singh, Chejin Bae, Byungwook Ahn, Kwang Oh, and Andrea Markelz. "Dynamical Alignment of Solution Phase Proteins for Structural Measurements." Biophysical Journal 100, no. 3 (2011): 224a. http://dx.doi.org/10.1016/j.bpj.2010.12.1434.

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14

Selenko, Philipp. "Quo Vadis Biomolecular NMR Spectroscopy?" International Journal of Molecular Sciences 20, no. 6 (2019): 1278. http://dx.doi.org/10.3390/ijms20061278.

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In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide br

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Ward, Abigail R., Sara Dmytriw, Ananya Vajapayajula, and Christopher D. Snow. "Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA." Crystals 12, no. 1 (2021): 49. http://dx.doi.org/10.3390/cryst12010049.

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Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide cros

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Grove, Tijana Z., Lynne Regan, and Aitziber L. Cortajarena. "Nanostructured functional films from engineered repeat proteins." Journal of The Royal Society Interface 10, no. 83 (2013): 20130051. http://dx.doi.org/10.1098/rsif.2013.0051.

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Fundamental advances in biotechnology, medicine, environment, electronics and energy require methods for precise control of spatial organization at the nanoscale. Assemblies that rely on highly specific biomolecular interactions are an attractive approach to form materials that display novel and useful properties. Here, we report on assembly of films from the designed, rod-shaped, superhelical, consensus tetratricopeptide repeat protein (CTPR). We have designed three peptide-binding sites into the 18 repeat CTPR to allow for further specific and non-covalent functionalization of films through

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PAI, TUN-WEN, RUEI-HSIANG CHANG, CHIEN-MING CHEN, et al. "MULTIPLE STRUCTURE ALIGNMENT BASED ON GEOMETRICAL CORRELATION OF SECONDARY STRUCTURE ELEMENTS." New Mathematics and Natural Computation 06, no. 01 (2010): 77–95. http://dx.doi.org/10.1142/s1793005710001621.

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Protein structure alignment facilitates the analysis of protein functionality. Through superimposed structures and the comparison of variant components, common or specific features of proteins can be identified. Several known protein families exhibit analogous tertiary structures but divergent primary sequences. These proteins in the same structural class are unable to be aligned by sequence-based methods. The main objective of the present study was to develop an efficient and effective algorithm for multiple structure alignment based on geometrical correlation of secondary structures, which a

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Murthy, Anastasia C., and Nicolas L. Fawzi. "The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy." Journal of Biological Chemistry 295, no. 8 (2020): 2375–84. http://dx.doi.org/10.1074/jbc.rev119.009847.

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Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a phenomenon that underlies membraneless compartmentalization of the cell. The underlying molecular interactions that underpin biomolecular LLPS have been of increased interest due to the importance of membraneless organelles in facilitating various biological processes and the disease association of several of the proteins that mediate LLPS. Proteins that are able to undergo LLPS often contain intrinsically disordered regions and remain dynamic in solution. Solution-state NMR spectroscopy has emerged as a leading structura

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Plewczynski, Dariusz, Jakub Pas, Marcin Von Grotthuss, and Leszek Rychlewski. "Comparison of proteins based on segments structural similarity." Acta Biochimica Polonica 51, no. 1 (2004): 161–72. http://dx.doi.org/10.18388/abp.2004_3608.

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We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Calpha chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity measure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolSh

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SALEM, SAEED, MOHAMMED J. ZAKI, and CHRISTOPHER BYSTROFF. "ITERATIVE NON-SEQUENTIAL PROTEIN STRUCTURAL ALIGNMENT." Journal of Bioinformatics and Computational Biology 07, no. 03 (2009): 571–96. http://dx.doi.org/10.1142/s0219720009004205.

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Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignmen

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Siu, Wing-Yan, Nikos Mamoulis, Siu-Ming Yiu, and Ho-Leung Chan. "A data-mining approach for multiple structural alignment of proteins." Bioinformation 4, no. 8 (2010): 366–70. http://dx.doi.org/10.6026/97320630004366.

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22

Sowdhamini, R., David F. Burke, Charlotte Deane, et al. "Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (1998): 1168–77. http://dx.doi.org/10.1107/s0907444998007148.

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This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the programDIAL[Sowdhamini & Blun

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23

Ding, Fei, and Wei Peng. "Biological activity of natural flavonoids as impacted by protein flexibility: an example of flavanones." Molecular BioSystems 11, no. 4 (2015): 1119–33. http://dx.doi.org/10.1039/c4mb00662c.

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The biomolecular recognition of typical flavanones, namely hesperidin and its aglycone hesperetin, by critical proteins has significant disparities, and these recognition distinctions may largely originate from the flexibility of protein structure and the structural characteristics of bioactive flavanones.

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Chakraborty, Arnab, Fabien Deligey, Jenny Quach, Frederic Mentink-Vigier, Ping Wang, and Tuo Wang. "Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy." Biochemical Society Transactions 48, no. 3 (2020): 1089–99. http://dx.doi.org/10.1042/bst20191084.

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Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and li

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Sangeeta and Anu Radha Pathania. "Circular dichroism and its uses in biomolecular research - A Review." E3S Web of Conferences 309 (2021): 01229. http://dx.doi.org/10.1051/e3sconf/202130901229.

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The higher-order structure of proteins as well as their thermal stability can be determined using the circular dichroism (CD). CD is a common approach for swiftly assessing binding, secondary structure, and folding properties of proteins. In a nutshell, circular dichroism is an absorption spectroscopy technique that employs circularly polarized light to explore structural properties of optically active chiral compounds. Biological molecules, as well as their interactions with metals and other compounds, are studied extensively. Circular dichroism is becoming more widely acknowledged as a usefu

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Lolkema, Juke S., and Dirk-Jan Slotboom. "Estimation of structural similarity of membrane proteins by hydropathy profile alignment." Molecular Membrane Biology 15, no. 1 (1998): 33–42. http://dx.doi.org/10.3109/09687689809027516.

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Micheletti, Cristian, and Henri Orland. "MISTRAL: a tool for energy-based multiple structural alignment of proteins." Bioinformatics 25, no. 20 (2009): 2663–69. http://dx.doi.org/10.1093/bioinformatics/btp506.

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28

Godzik, Adam. "The structural alignment between two proteins: Is there a unique answer?" Protein Science 5, no. 7 (1996): 1325–38. http://dx.doi.org/10.1002/pro.5560050711.

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Li, Zhanwen, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, and Adam Godzik. "FATCAT 2.0: towards a better understanding of the structural diversity of proteins." Nucleic Acids Research 48, W1 (2020): W60—W64. http://dx.doi.org/10.1093/nar/gkaa443.

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Abstract FATCAT 2.0 server (http://fatcat.godziklab.org/), provides access to a flexible protein structure alignment algorithm developed in our group. In such an alignment, rotations and translations between elements in the structure are allowed to minimize the overall root mean square deviation (RMSD) between the compared structures. This allows to effectively compare protein structures even if they underwent structural rearrangements in different functional forms, different crystallization conditions or as a result of mutations. The major update for the server introduces a new graphical inte

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Briggs, Derek E. G., Richard P. Evershed, and Matthew J. Lockheart. "The biomolecular paleontology of continental fossils." Paleobiology 26, S4 (2000): 169–93. http://dx.doi.org/10.1017/s0094837300026920.

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The preservation of compounds of biological origin (nucleic acids, proteins, carbohydrates, lipids, and resistant biopolymers) in terrigenous fossils and the chemical and structural changes that they undergo during fossilization are discussed over three critical stratigraphic levels or “time slices.” The youngest of these is the archeological record (e.g., <10 k.y. B.P.), when organic matter from living organisms undergoes the preliminary stages of fossilization (certain classes of biomolecule are selectively preserved while others undergo rapid degradation). The second time slice is the Te

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Mukhopadhyay, Samrat. "Shapeshifting proteins: the role of structural disorder and conformational plasticity in physiology and disease." Essays in Biochemistry 66, no. 7 (2022): 817–19. http://dx.doi.org/10.1042/ebc20220197.

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Abstract Intrinsically disordered proteins (IDPs) defy the conventional structure–function paradigm and do not autonomously fold up into unique 3D structures for carrying out functions. They exist as rapidly interconverting conformational ensembles and are thought to expand the functional repertoire of proteins. Such shapeshifting proteins are associated with a multitude of biological functions and a wide range of human diseases. The thematic issue on ‘Shapeshifting Proteins’ in Essays in Biochemistry includes some exciting and emerging aspects of this class of proteins. Articles in this issue

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Mirzaei, Soraya, Jafar Razmara, and Shahriar Lotfi. "GADP-align: A genetic algorithm and dynamic programming-based method for structural alignment of proteins." BioImpacts 11, no. 4 (2020): 271–79. http://dx.doi.org/10.34172/bi.2021.37.

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Introduction: Similarity analysis of protein structure is considered as a fundamental step to give insight into the relationships between proteins. The primary step in structural alignment is looking for the optimal correspondence between residues of two structures to optimize the scoring function. An exhaustive search for finding such a correspondence between two structures is intractable. Methods: In this paper, a hybrid method is proposed, namely GADP-align, for pairwise protein structure alignment. The proposed method looks for an optimal alignment using a hybrid method based on a genetic

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Reeck, Gerald R., and Charles Hedgcoth. "Amino acid sequence alignment of cereal storage proteins." FEBS Letters 180, no. 2 (1985): 291–94. http://dx.doi.org/10.1016/0014-5793(85)81088-7.

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Razmara, Jafar. "A Method for Multiple Structural Alignment of Proteins Using Text Modeling Techniques." International Journal of Future Computer and Communication 4, no. 2 (2015): 143–46. http://dx.doi.org/10.7763/ijfcc.2015.v4.373.

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Katrusiak, Andrzej, Michalina Aniola, Kamil Dziubek, Kinga Ostrowska, and Ewa Patyk. "Biomolecular systems under pressure." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1188. http://dx.doi.org/10.1107/s2053273314088111.

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Biological systems are often regarded as the ultimate goal of all knowledge in this respect that they can provide the clue for understanding the origin of life and the means for improving the life conditions and healthcare. Hence the interest in high-pressure behavior of organic and biomolecular systems. Such simple organic systems were among the first structural studies at high pressure at all. They included chloroform by Roger Fourme in 1968 [1] and benzene by Piermarini et al. in 1969, still with the use of photographic technique. The efficient studies on bio-macromolecular crystals had to

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Wu, Yueh-Fu O., Annamarie T. Bryant, Nora T. Nelson, Alexander G. Madey, Gail F. Fernandes, and Holly V. Goodson. "Overexpression of the microtubule-binding protein CLIP-170 induces a +TIP network superstructure consistent with a biomolecular condensate." PLOS ONE 16, no. 12 (2021): e0260401. http://dx.doi.org/10.1371/journal.pone.0260401.

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Proper regulation of microtubule (MT) dynamics is critical for cellular processes including cell division and intracellular transport. Plus-end tracking proteins (+TIPs) dynamically track growing MTs and play a key role in MT regulation. +TIPs participate in a complex web of intra- and inter- molecular interactions known as the +TIP network. Hypotheses addressing the purpose of +TIP:+TIP interactions include relieving +TIP autoinhibition and localizing MT regulators to growing MT ends. In addition, we have proposed that the web of +TIP:+TIP interactions has a physical purpose: creating a dynam

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Ferrage, Fabien, Kaushik Dutta, Alexander Shekhtman, and David Cowburn. "Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density." Journal of Biomolecular NMR 47, no. 1 (2010): 41–54. http://dx.doi.org/10.1007/s10858-010-9409-9.

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Errami, Mounir, Christophe Geourjon, and Gilbert Deléage. "Conservation of Amino Acids into Multiple Alignments Involved in Pairwise Interactions in Three-Dimensional Protein Structures." Journal of Bioinformatics and Computational Biology 01, no. 03 (2003): 505–20. http://dx.doi.org/10.1142/s0219720003000228.

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We present an original strategy, that involves a bioinformatic software structure, in order to perform an exhaustive and objective statistical analysis of three-dimensional structures of proteins. We establish the relationship between multiple sequences alignments and various structural features of proteins. We show that amino acids implied in disulfide bonds, salt bridges and hydrophobic interactions are particularly conserved. Effects of identity, global similarity within alignments, and accessibility of interactions have been studied. Furthermore, we point out that the more variable the seq

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POLEKSIC, ALEKSANDAR. "OPTIMAL PAIRWISE ALIGNMENT OF FIXED PROTEIN STRUCTURES IN SUBQUADRATIC TIME." Journal of Bioinformatics and Computational Biology 09, no. 03 (2011): 367–82. http://dx.doi.org/10.1142/s0219720011005562.

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The problem of finding an optimal structural alignment for a pair of superimposed proteins is often amenable to the Smith–Waterman dynamic programming algorithm, which runs in time proportional to the product of lengths of the sequences being aligned. While the quadratic running time is acceptable for computing a single alignment of two fixed protein structures, the time complexity becomes a bottleneck when running the Smith–Waterman routine multiple times in order to find a globally optimal superposition and alignment of the input proteins. We present a subquadratic running time algorithm cap

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Muniyappan, Srinivasan, Yuxi Lin, Young-Ho Lee, and Jin Hae Kim. "17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding." Biology 10, no. 6 (2021): 453. http://dx.doi.org/10.3390/biology10060453.

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Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3)

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Sreemantula, Arun Kumar, and Alexander Marchanka. "Solid-state NMR spectroscopy for characterization of RNA and RNP complexes." Biochemical Society Transactions 48, no. 3 (2020): 1077–87. http://dx.doi.org/10.1042/bst20191080.

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Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA an

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Liu, Hui, Jie Yang, Dan-Qing Liu, Hong-Bin Shen, and Kuo-Chen Chou. "Using a New Alignment Kernel Function to Identify Secretory Proteins." Protein & Peptide Letters 14, no. 2 (2007): 203–8. http://dx.doi.org/10.2174/092986607779816087.

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Amyot, Romain, and Holger Flechsig. "BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics." PLOS Computational Biology 16, no. 11 (2020): e1008444. http://dx.doi.org/10.1371/journal.pcbi.1008444.

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We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the a

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Tyagi, Manoj, Venkataraman S. Gowri, Narayanaswamy Srinivasan, Alexandre G. de Brevern, and Bernard Offmann. "A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications." Proteins: Structure, Function, and Bioinformatics 65, no. 1 (2006): 32–39. http://dx.doi.org/10.1002/prot.21087.

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Staritzbichler, René, Edoardo Sarti, Emily Yaklich, et al. "Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors." PLOS ONE 16, no. 4 (2021): e0239881. http://dx.doi.org/10.1371/journal.pone.0239881.

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The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently

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Huang, Yen-Hua, and Cheng-Yang Huang. "Structural Insight into the DNA-Binding Mode of the Primosomal Proteins PriA, PriB, and DnaT." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/195162.

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Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome inEscherichia coliis composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over

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Voronin, Arthur, and Alexander Schug. "Selection of representative structures from large biomolecular ensembles." Journal of Chemical Physics 156, no. 14 (2022): 144102. http://dx.doi.org/10.1063/5.0082444.

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Despite the incredible progress of experimental techniques, protein structure determination still remains a challenging task. Due to the rapid improvements of computer technology, simulations are often used to complement or interpret experimental data, particularly for sparse or low-resolution data. Many such in silico methods allow us to obtain highly accurate models of a protein structure either de novo or via refinement of a physical model with experimental restraints. One crucial question is how to select a representative member or ensemble out of the vast number of computationally generat

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Trewhella, Jill, Cy M. Jeffries, and Andrew E. Whitten. "2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data." Acta Crystallographica Section D Structural Biology 79, no. 2 (2023): 122–32. http://dx.doi.org/10.1107/s2059798322012141.

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In 2017, guidelines were published for reporting structural modelling of small-angle scattering (SAS) data from biomolecules in solution that exemplified best-practice documentation of experiments and analysis. Since then, there has been significant progress in SAS data and model archiving, and the IUCr journal editors announced that the IUCr biology journals will require the deposition of SAS data used in biomolecular structure solution into a public archive, as well as adherence to the 2017 reporting guidelines. In this context, the reporting template tables accompanying the 2017 publication

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Noel, Jeffrey K., Faruck Morcos, and Jose N. Onuchic. "Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics." F1000Research 5 (January 26, 2016): 106. http://dx.doi.org/10.12688/f1000research.7186.1.

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Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Str

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Cafferkey, Robert, Megan M. McLaughlin, Peter R. Young, Randall K. Johnson, and George P. Livi. "Yeast TOR (DRR) proteins: amino-acid sequence alignment and identification of structural motifs." Gene 141, no. 1 (1994): 133–36. http://dx.doi.org/10.1016/0378-1119(94)90141-4.

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