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Journal articles on the topic 'Protein conformation'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Cresti, Julianna R., Abramo J. Manfredonia, Christopher E. Bragança, et al. "Proteasomal conformation controls unfolding ability." Proceedings of the National Academy of Sciences 118, no. 25 (2021): e2101004118. http://dx.doi.org/10.1073/pnas.2101004118.

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The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions

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2

Ohhashi, Yumiko, Yoshiki Yamaguchi, Hiroshi Kurahashi, et al. "Molecular basis for diversification of yeast prion strain conformation." Proceedings of the National Academy of Sciences 115, no. 10 (2018): 2389–94. http://dx.doi.org/10.1073/pnas.1715483115.

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Self-propagating β-sheet–rich fibrillar protein aggregates, amyloid fibers, are often associated with cellular dysfunction and disease. Distinct amyloid conformations dictate different physiological consequences, such as cellular toxicity. However, the origin of the diversity of amyloid conformation remains unknown. Here, we suggest that altered conformational equilibrium in natively disordered monomeric proteins leads to the adaptation of alternate amyloid conformations that have different phenotypic effects. We performed a comprehensive high-resolution structural analysis of Sup35NM, an N-te

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3

Cretin, Gabriel, Tatiana Galochkina, Alexandre G. de Brevern, and Jean-Christophe Gelly. "PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction." International Journal of Molecular Sciences 22, no. 16 (2021): 8831. http://dx.doi.org/10.3390/ijms22168831.

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Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1D PB sequences was previously successfully applied to protein structure alignment and protein structure prediction. In the current study, we present a new model, PYTHIA (predicting any conformation at high accuracy), for the prediction of the protein local conformations in terms of PBs directly from the amino acid sequence. PYTHIA is based on a dee

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4

Seo, Udeok, Ku-Jin Kim, and Beom Kang. "An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel." Molecules 23, no. 10 (2018): 2459. http://dx.doi.org/10.3390/molecules23102459.

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In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are c

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5

Merski, Matthew, Marcus Fischer, Trent E. Balius, Oliv Eidam, and Brian K. Shoichet. "Homologous ligands accommodated by discrete conformations of a buried cavity." Proceedings of the National Academy of Sciences 112, no. 16 (2015): 5039–44. http://dx.doi.org/10.1073/pnas.1500806112.

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Conformational change in protein–ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformat

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6

DOWNING, Donald T., та N. D. LAZO. "Molecular modelling indicates that the pathological conformations of prion proteins might be β-helical". Biochemical Journal 343, № 2 (1999): 453–60. http://dx.doi.org/10.1042/bj3430453.

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Creutzfeldt-Jakob disease, kuru, scrapie and bovine spongiform encephalopathy are diseases of the mammalian central nervous system that involve the conversion of a cellular protein into an insoluble extracellular isoform. Spectroscopic studies have shown that the precursor protein contains mainly α-helical and random-coil conformations, whereas the prion isoform is largely in the β conformation. The pathogenic prion is resistant to denaturation and protease digestion and can promote the conversion of the precursor protein to the pathogenic form. These properties have yet to be explained in ter

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7

Avdeev, P. A., V. A. Ignatenko, Yu V. Kornoushenko, and L. A. Evtuhova. "EFFECT OF DIFFERENT CONCENTRATIONS OF UREA AND PH ON THE FLUORESCENCE PARAMETERS OF BOVINE SERUM ALBUMIN." Health and Ecology Issues, no. 1 (March 28, 2011): 106–10. http://dx.doi.org/10.51523/2708-6011.2011-8-1-20.

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Urea is a chemical effect on the conformation of bovine serum albumin, causing a partial unfolding of the protein globule its exit to the surface of hydrophobic amino acids. Changing the pH of the solution in which the protein also affects the state of the protein, so there are multiple conformational states in which urea as a chemical effect on the conformation of bovine serum albumin, causing a partial unfolding of the protein globule of its exit to the surface of hydrophobic amino acids. Changing the pH of the solution in which the protein also affects the state of the protein, so there are

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8

Giri Rao, V. V. Hemanth, and Shachi Gosavi. "On the folding of a structurally complex protein to its metastable active state." Proceedings of the National Academy of Sciences 115, no. 9 (2018): 1998–2003. http://dx.doi.org/10.1073/pnas.1708173115.

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For successful protease inhibition, the reactive center loop (RCL) of the two-domain serine protease inhibitor, α1-antitrypsin (α1-AT), needs to remain exposed in a metastable active conformation. The α1-AT RCL is sequestered in a β-sheet in the stable latent conformation. Thus, to be functional, α1-AT must always fold to a metastable conformation while avoiding folding to a stable conformation. We explore the structural basis of this choice using folding simulations of coarse-grained structure-based models of the two α1-AT conformations. Our simulations capture the key features of folding exp

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9

Mizutani, Tadashi, and Shigeyuki Yagi. "Linear tetrapyrroles as functional pigments in chemistry and biology." Journal of Porphyrins and Phthalocyanines 08, no. 03 (2004): 226–37. http://dx.doi.org/10.1142/s1088424604000210.

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1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally

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10

Egorov, Vladimir, Natalia Grudinina, Andrey Vasin, and Dmitry Lebedev. "Peptide-Induced Amyloid-Like Conformational Transitions in Proteins." International Journal of Peptides 2015 (September 8, 2015): 1–5. http://dx.doi.org/10.1155/2015/723186.

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Changes in protein conformation can occur both as part of normal protein functioning and during disease pathogenesis. The most common conformational diseases are amyloidoses. Sometimes the development of a number of diseases which are not traditionally related to amyloidoses is associated with amyloid-like conformational transitions of proteins. Also, amyloid-like aggregates take part in normal physiological processes such as memorization and cell signaling. Several primary structural features of a protein are involved in conformational transitions. Also the protein proteolytic fragments can c

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11

Solopova, O. N., L. P. Pozdnyakova, N. E. Varlamov, et al. "Conformational Differences between Active Angiotensins and Their Inactive Precursors." Acta Naturae 4, no. 1 (2012): 74–77. http://dx.doi.org/10.32607/20758251-2012-4-1-74-77.

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The peptide conformation in the context of a protein polypeptide chain is influenced by proximal amino acid residues. However, the mechanisms of this interference remain poorly understood. We studied the conformation of angiotensins 1, 2 and 3, which are produced naturally in a sequential fashion from a precursor protein angiotensinogen and contain an identical peptide core structure. Using the example of angiotensins 1, 2 and 3, it was shown that similar amino acid sequences may have significant conformational differences in various molecules. In order to assess the conformational changes, we

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12

Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic та ін. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR". Proceedings of the National Academy of Sciences 112, № 46 (2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

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Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like re

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13

Almahmoud, Suliman, Xiaofang Wang, Jonathan L. Vennerstrom, and Haizhen A. Zhong. "Conformational Studies of Glucose Transporter 1 (GLUT1) as an Anticancer Drug Target." Molecules 24, no. 11 (2019): 2159. http://dx.doi.org/10.3390/molecules24112159.

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Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand bindi

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14

Serio, Tricia R., Anil G. Cashikar, Anthony S. Kowal, George J. Sawicki, and Susan L. Lindquist. "Self-perpetuating changes in Sup35 protein conformation as a mechanism of heredity in yeast." Biochemical Society Symposia 68 (August 1, 2001): 35–43. http://dx.doi.org/10.1042/bss0680035.

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Recently, a novel mode of inheritance has been described in the yeast Saccharomyces cerevisiae. The mechanism is based on the prion hypothesis, which posits that self-perpetuating changes in the conformation of single protein, PrP, underlie the severe neurodegeneration associated with the transmissible spongiform enchephalopathies in mammals. In yeast, two prions, [URE3] and [PSI+], have been identified, but these factors confer unique phenotypes rather than disease to the organism. In each case, the prion-associated phenotype has been linked to alternative conformations of the Ure2 and Sup35

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15

Roh, Soung-Hun, Corey F. Hryc, Hyun-Hwan Jeong, et al. "Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM." Proceedings of the National Academy of Sciences 114, no. 31 (2017): 8259–64. http://dx.doi.org/10.1073/pnas.1704725114.

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Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Pro

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16

Mary, Sophie, Jean-Alain Fehrentz, Marjorie Damian, et al. "How ligands and signalling proteins affect G-protein-coupled receptors' conformational landscape." Biochemical Society Transactions 41, no. 1 (2013): 144–47. http://dx.doi.org/10.1042/bst20120267.

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The dynamic character of GPCRs (G-protein-coupled receptors) is essential to their function. However, the details of how ligands and signalling proteins stabilize a receptor conformation to trigger the activation of a given signalling pathway remain largely unexplored. Multiple data, including recent results obtained with the purified ghrelin receptor, suggest a model where ligand efficacy and functional selectivity are directly related to different receptor conformations. Importantly, distinct effector proteins (G-proteins and arrestins) as well as ligands are likely to affect the conformatio

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17

Nakae, Setsu, Maho Kitamura, Daisuke Fujiwara, et al. "Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation." Acta Crystallographica Section F Structural Biology Communications 77, no. 12 (2021): 459–64. http://dx.doi.org/10.1107/s2053230x21011687.

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Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38–381) complexed with ATP-γS is reported in which MEK1 ado

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18

Sun, Shangwu, Rui Zhu, Mengyao Zhu, Qi Wang, Na Li, and Bei Yang. "Visualization of conformational transition of GRP94 in solution." Life Science Alliance 7, no. 2 (2023): e202302051. http://dx.doi.org/10.26508/lsa.202302051.

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GRP94, an ER paralog of the heat-shock protein 90 family, binds and hydrolyses ATP to chaperone the folding and maturation of its selected clients. Compared with other hsp90 proteins, the in-solution conformational dynamics of GRP94 along the ATP hydrolysis cycle are less understood, hindering our understanding of its chaperoning mechanism. Leveraging small-angle X-ray scattering, negative-staining EM, and hydrogen–deuterium exchange coupled mass-spec, here we show that in its apo form, ∼60% of mouse GRP94 (mGRP94) populates an “extended” conformation, whereas the rest exist in either “close V

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19

Guo, Qing, Yufan He, and H. Peter Lu. "Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy." Proceedings of the National Academy of Sciences 112, no. 45 (2015): 13904–9. http://dx.doi.org/10.1073/pnas.1506405112.

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Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we succe

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20

Ramm, Ingrid, Adrian Sanchez-Fernandez, Jaeyeong Choi, et al. "The Impact of Glycerol on an Affibody Conformation and Its Correlation to Chemical Degradation." Pharmaceutics 13, no. 11 (2021): 1853. http://dx.doi.org/10.3390/pharmaceutics13111853.

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The addition of glycerol to protein solutions is often used to hinder the aggregation and denaturation of proteins. However, it is not a generalised practice against chemical degradation reactions. The chemical degradation of proteins, such as deamidation and isomerisation, is an important deteriorative mechanism that leads to a loss of functionality of pharmaceutical proteins. Here, the influence of glycerol on the chemical degradation of a protein and its correlation to glycerol-induced conformational changes is presented. The time-dependent chemical degradation of a pharmaceutical protein,

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21

Garaizar, Adiran, Ignacio Sanchez-Burgos, Rosana Collepardo-Guevara, and Jorge R. Espinosa. "Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation." Molecules 25, no. 20 (2020): 4705. http://dx.doi.org/10.3390/molecules25204705.

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Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid–liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, incl

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22

LEE, HO-JIN, HYUN-MEE PARK, and KANG-BONG LEE. "CONFORMATIONAL PREFERENCES OF N-ACETYL–GLYCINE–GLYCINE–N′-METHYLAMIDE: A THEORETICAL STUDY." Journal of Theoretical and Computational Chemistry 08, no. 05 (2009): 799–811. http://dx.doi.org/10.1142/s0219633609005118.

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The conformational preferences of peptide models have been investigated to understand the protein folding mechanism and to develop the force field. Here, we report the minimum energy conformations for a model peptide, N-acetyl–glycine–glycine–N′-methylamide ( Ac–1Gly–2Gly–NHMe(I) ) at the HF/3-21G, HF/6-31G*, and the B3LYP/6-31G* level of theory. At the B3LYP/6-31G* level, the 31 minima were identified and the 10 β-turn structures among the minima were observed in gas-phase. The conformational preferences of Gly residue in the model peptide, I depend on its relative position and conformation o

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23

Cahill, Thomas J., Alex R. B. Thomsen, Jeffrey T. Tarrasch та ін. "Distinct conformations of GPCR–β-arrestin complexes mediate desensitization, signaling, and endocytosis". Proceedings of the National Academy of Sciences 114, № 10 (2017): 2562–67. http://dx.doi.org/10.1073/pnas.1701529114.

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β-Arrestins (βarrs) interact with G protein-coupled receptors (GPCRs) to desensitize G protein signaling, to initiate signaling on their own, and to mediate receptor endocytosis. Prior structural studies have revealed two unique conformations of GPCR–βarr complexes: the “tail” conformation, with βarr primarily coupled to the phosphorylated GPCR C-terminal tail, and the “core” conformation, where, in addition to the phosphorylated C-terminal tail, βarr is further engaged with the receptor transmembrane core. However, the relationship of these distinct conformations to the various functions of β

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Li, Haiyan, Zanxia Cao, Guodong Hu, Liling Zhao, Chunling Wang, and Jihua Wang. "Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations." Technology and Health Care 29 (March 25, 2021): 103–14. http://dx.doi.org/10.3233/thc-218011.

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BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models.

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Guerrini, Giuditta, Dora Mehn, Francesco Fumagalli, et al. "Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer." International Journal of Molecular Sciences 24, no. 19 (2023): 14875. http://dx.doi.org/10.3390/ijms241914875.

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Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the “open” and “close” conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, whi

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Kulichikhin, Konstantin Y., Oksana A. Malikova, Anastasia E. Zobnina, Natalia M. Zalutskaya, and Aleksandr A. Rubel. "Interaction of Proteins Involved in Neuronal Proteinopathies." Life 13, no. 10 (2023): 1954. http://dx.doi.org/10.3390/life13101954.

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Proteinopathy is characterized by the accumulation of aggregates of a specific protein in a target organ, tissue, or cell. The aggregation of the same protein can cause different pathologies as single protein can adopt various amyloidogenic, disease-specific conformations. The conformation governs the interaction of amyloid aggregates with other proteins that are prone to misfolding and, thus, determines disease-specific spectrum of concomitant pathologies. In this regard, a detailed description of amyloid protein conformation as well as spectrum of its interaction with other proteins become a

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Joshi, Arpita, Nurit Haspel, and Eduardo González. "Characterizing Protein Conformational Spaces using Efficient Data Reduction and Algebraic Topology." Journal of Human, Earth, and Future 3 (May 31, 2022): 1–21. http://dx.doi.org/10.28991/hef-sp2022-01-01.

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Datasets representing the conformational landscapes of protein structures are high-dimensional and hence present computational challenges. Efficient and effective dimensionality reduction of these datasets is therefore paramount to our ability to analyze the conformational landscapes of proteins and extract important information regarding protein folding, conformational changes, and binding. Representing the structures with fewer attributes that capture the most variance in the data makes for a quicker and more precise analysis of these structures. In this study, we make use of dimensionality

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28

Lin, Shawn H., Dacheng Zhao, Vivian Deng, et al. "Integration Host Factor Binds DNA Holliday Junctions." International Journal of Molecular Sciences 24, no. 1 (2022): 580. http://dx.doi.org/10.3390/ijms24010580.

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Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF binds to DNA Four-way or Holliday junctions (HJ) with high affinity regardless of the presence of the consensus sequence, signifying a structure-based mechanism of recognition. Junctions, important intermediates in DNA repair and homologous recombination, are dynamic and can adopt either an open or stacked conformat

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29

Moore, Alexander F., David J. Newman, Shoba Ranganathan, and Fei Liu. "Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions." Australian Journal of Chemistry 71, no. 12 (2018): 917. http://dx.doi.org/10.1071/ch18416.

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Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive

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Lerch, Michael T., Rachel A. Matt, Matthieu Masureel та ін. "Viewing rare conformations of the β2 adrenergic receptor with pressure-resolved DEER spectroscopy". Proceedings of the National Academy of Sciences 117, № 50 (2020): 31824–31. http://dx.doi.org/10.1073/pnas.2013904117.

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The β2 adrenergic receptor (β2AR) is an archetypal G protein coupled receptor (GPCR). One structural signature of GPCR activation is a large-scale movement (ca. 6 to 14 Å) of transmembrane helix 6 (TM6) to a conformation which binds and activates a cognate G protein. The β2AR exhibits a low level of agonist-independent G protein activation. The structural origin of this basal activity and its suppression by inverse agonists is unknown but could involve a unique receptor conformation that promotes G protein activation. Alternatively, a conformational selection model proposes that a minor popula

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Xiao, Qingjie, Mengxue Xu, Weiwei Wang, et al. "Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation." International Journal of Molecular Sciences 23, no. 13 (2022): 7235. http://dx.doi.org/10.3390/ijms23137235.

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The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanism, it is necessary to obtain structures of these different conformations. At present, great progress has been made in predicting protein structure based on coevolutionary information. In this study, AlphaFold2 was used to predict different conformational structures for 69 MFS transporters of E. coli

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Indergaard, John, Matthew McLeod, Robert Thorne, and Todd Holyoak. "High-pressure room-temperature crystallography reveals catalytic lid dynamics even in the absence of ligands." Structural Dynamics 12, no. 2_Supplement (2025): A266. https://doi.org/10.1063/4.0000572.

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Enzymes undergo local and large-scale conformational changes as required to execute each step in their catalytic cycle. Typically, ligand binding and establishment of all protein-ligand interactions generates new protein conformations essential to the chemical transformation. Without the ligand interactions, apo protein crystals often do not have sufficient interactions/bonds to adopt the catalytically “ready” conformation, an obstacle to structural studies when in crystallo binding is not possible. We have explored the use of pressure to perturb interactions and the energy landscape so as to

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GUYEUX, CHRISTOPHE, NATHALIE M. L. CÔTÉ, JACQUES M. BAHI, and WOJCIECH BIENIA. "IS PROTEIN FOLDING PROBLEM REALLY A NP-COMPLETE ONE? FIRST INVESTIGATIONS." Journal of Bioinformatics and Computational Biology 12, no. 01 (2014): 1350017. http://dx.doi.org/10.1142/s0219720013500170.

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To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D conformations, they tend to choose the ones that minimize their free energy. To find the 3D conformation of a protein knowing its amino acid sequence, bioinformaticians use various models of different resolutions and artificial intelligence tools, as the protein folding prediction problem is a NP complete one. More precisely, to determine the backbone structure of t

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Fischer, Marion F. S., James E. Crowe, and Jens Meiler. "Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods." PLOS Computational Biology 18, no. 12 (2022): e1010230. http://dx.doi.org/10.1371/journal.pcbi.1010230.

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Antibody epitope mapping of viral proteins plays a vital role in understanding immune system mechanisms of protection. In the case of class I viral fusion proteins, recent advances in cryo-electron microscopy and protein stabilization techniques have highlighted the importance of cryptic or ‘alternative’ conformations that expose epitopes targeted by potent neutralizing antibodies. Thorough epitope mapping of such metastable conformations is difficult but is critical for understanding sites of vulnerability in class I fusion proteins that occur as transient conformational states during viral a

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Pasala, Chiranjeevi, Sahil Sharma, Tanaya Roychowdhury, Elisabetta Moroni, Giorgio Colombo, and Gabriela Chiosis. "N-Glycosylation as a Modulator of Protein Conformation and Assembly in Disease." Biomolecules 14, no. 3 (2024): 282. http://dx.doi.org/10.3390/biom14030282.

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Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing cancer, neurodegenerative disorders, congenital disorders, infections, and inflammation. This review delves into the intricate interplay between glycosylation and protein conformation, with a specific focus on the profound impact of N-glycans on the selection of distinct protein conformations characterized by distinct interactomes—namely, protein

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Ludwiczak, Jan, Ewa Szczęsna, Antônio Marinho da Silva Neto, Piotr Cieplak, Andrzej A. Kasprzak, and Adam Jarmuła. "Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study." Biochemical Journal 476, no. 17 (2019): 2449–62. http://dx.doi.org/10.1042/bcj20190484.

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Abstract Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-st

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Fernández-Quintero, Monica L., Martin C. Heiss, and Klaus R. Liedl. "Antibody humanization—the Influence of the antibody framework on the CDR-H3 loop ensemble in solution." Protein Engineering, Design and Selection 32, no. 9 (2019): 411–22. http://dx.doi.org/10.1093/protein/gzaa004.

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Abstract Antibody engineering of non-human antibodies has focused on reducing immunogenicity by humanization, being a major limitation in developing monoclonal antibodies. We analyzed four series of antibody binding fragments (Fabs) and a variable fragment (Fv) with structural information in different stages of humanization to investigate the influence of the framework, point mutations and specificity on the complementarity determining region (CDR)-H3 loop dynamics. We also studied a Fv without structural information of the anti-idiotypic antibody Ab2/3H6, because it completely lost its bindin

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Toepfer, Christopher N., Amanda C. Garfinkel, Gabriela Venturini, et al. "Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy." Circulation 141, no. 10 (2020): 828–42. http://dx.doi.org/10.1161/circulationaha.119.042339.

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Background: Hypertrophic cardiomyopathy (HCM) is caused by pathogenic variants in sarcomere protein genes that evoke hypercontractility, poor relaxation, and increased energy consumption by the heart and increased patient risks for arrhythmias and heart failure. Recent studies show that pathogenic missense variants in myosin, the molecular motor of the sarcomere, are clustered in residues that participate in dynamic conformational states of sarcomere proteins. We hypothesized that these conformations are essential to adapt contractile output for energy conservation and that pathophysiology of

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Kang, Hyun-Seo, and Michael Sattler. "Capturing dynamic conformational shifts in protein–ligand recognition using integrative structural biology in solution." Emerging Topics in Life Sciences 2, no. 1 (2018): 107–19. http://dx.doi.org/10.1042/etls20170090.

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In recent years, a dynamic view of the structure and function of biological macromolecules is emerging, highlighting an essential role of dynamic conformational equilibria to understand molecular mechanisms of biological functions. The structure of a biomolecule, i.e. protein or nucleic acid in solution, is often best described as a dynamic ensemble of conformations, rather than a single structural state. Strikingly, the molecular interactions and functions of the biological macromolecule can then involve a shift between conformations that pre-exist in such an ensemble. Upon external cues, suc

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Yagi-Utsumi, Maho, та Koichi Kato. "Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates". Molecules 27, № 15 (2022): 4787. http://dx.doi.org/10.3390/molecules27154787.

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Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and

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Gül, Nadir, and Ahmet Yıldız. "An in silico study of how histone tail conformation affects the binding affinity of ING family proteins." PeerJ 10 (September 30, 2022): e14029. http://dx.doi.org/10.7717/peerj.14029.

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Background Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone

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Shi, Heping, Jiaxi Wu, Zhijian J. Chen, and Chuo Chen. "Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING." Proceedings of the National Academy of Sciences 112, no. 29 (2015): 8947–52. http://dx.doi.org/10.1073/pnas.1507317112.

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Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2′3′-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2′3′-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. Here we show that 2′3′-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and entha

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Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.

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The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked

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Camacho, Inês S., Alina Theisen, Linus O. Johannissen, et al. "Native mass spectrometry reveals the conformational diversity of the UVR8 photoreceptor." Proceedings of the National Academy of Sciences 116, no. 4 (2019): 1116–25. http://dx.doi.org/10.1073/pnas.1813254116.

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UVR8 is a plant photoreceptor protein that regulates photomorphogenic and protective responses to UV light. The inactive, homodimeric state absorbs UV-B light, resulting in dissociation into monomers, which are considered to be the active state and comprise a β-propeller core domain and intrinsically disordered N- and C-terminal tails. The C terminus is required for functional binding to signaling partner COP1. To date, however, structural studies have only been conducted with the core domain where the terminal tails have been truncated. Here, we report structural investigations of full-length

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Wisniewski, T., D. R. Brown, and E. M. Sigurdsson. "Therapeutics in Alzheimer's and Prion Diseases." Biochemical Society Transactions 30, no. 4 (2002): 574–78. http://dx.doi.org/10.1042/bst0300574.

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There is increasing recognition that numerous neurodegenerative conditions have the same underlying pathogenetic mechanism, namely a change in protein conformation, where the β-sheet content is increased. In Alzheimer's disease, amyloid deposition in the form of neuritic plaques and congophilic angiopathy is driven by the conversion of normal soluble amyloid-β peptide (sAβ) to Aβ plaques; while in the prionoses the critical event is the conversion of normal prion protein, PrPc, to the disease-associated form, PrPsc. This common theme in the pathogenesis of these disorders and the extracellular

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Cai, Dawen, Adam D. Hoppe, Joel A. Swanson, and Kristen J. Verhey. "Kinesin-1 structural organization and conformational changes revealed by FRET stoichiometry in live cells." Journal of Cell Biology 176, no. 1 (2007): 51–63. http://dx.doi.org/10.1083/jcb.200605097.

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Kinesin motor proteins drive the transport of cellular cargoes along microtubule tracks. How motor protein activity is controlled in cells is unresolved, but it is likely coupled to changes in protein conformation and cargo association. By applying the quantitative method fluorescence resonance energy transfer (FRET) stoichiometry to fluorescent protein (FP)–labeled kinesin heavy chain (KHC) and kinesin light chain (KLC) subunits in live cells, we studied the overall structural organization and conformation of Kinesin-1 in the active and inactive states. Inactive Kinesin-1 molecules are folded

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Golderg, M. "Protein Conformation." Biochimie 74, no. 2 (1992): 211–12. http://dx.doi.org/10.1016/0300-9084(92)90056-k.

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Kim, J. I., K. Eom, and S. Na. "Mechanical Mass-Spring Model for Understanding Globular Motion of Proteins." Journal of Mechanics 32, no. 2 (2016): 123–29. http://dx.doi.org/10.1017/jmech.2015.109.

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AbstractThe conformational (structural) change of proteins plays an essential role in their functions. Experiments have been conducted to try to understand the conformational change of proteins, but they have not been successful in providing information on the atomic scale. Simulation methods have been developed to understand the conformational change at an atomic scale in detail. Coarse-grained methods have been developed to calculate protein dynamics with computational efficiency when compared with than all-atom models. A structure-based mass-spring model called the elastic network model (EN

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Campbell, Ashley C., Kyle M. Stiers, Julia S. Martin Del Campo, Ritcha Mehra-Chaudhary, Pablo Sobrado, and John J. Tanner. "Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics." Journal of Biological Chemistry 295, no. 38 (2020): 13239–49. http://dx.doi.org/10.1074/jbc.ra120.014750.

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The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N-monooxygenase that catalyzes the NADPH-dependent hydroxylation of l-ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l-ornithine bound (re

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Yeung, Heidi O., Andreas Förster, Cecilia Bebeacua, et al. "Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy." Open Biology 4, no. 3 (2014): 130142. http://dx.doi.org/10.1098/rsob.130142.

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The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, w

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