scholarly journals Solution structure of a defensin-like peptide from platypus venom

1999 ◽  
Vol 341 (3) ◽  
pp. 785-794 ◽  
Author(s):  
Allan M. TORRES ◽  
Xiuhong WANG ◽  
Jamie I. FLETCHER ◽  
Dianne ALEWOOD ◽  
Paul F. ALEWOOD ◽  
...  
Keyword(s):  
Sodium Channel ◽  
Dorsal Root ◽  
Solution Structure ◽  
Biological Function ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Elements ◽  
Channel Currents ◽  
Β Sheet ◽  
310 Helix

Three defensin-like peptides (DLPs) were isolated from platypus venom and sequenced. One of these peptides, DLP-1, was synthesized chemically and its three-dimensional structure was determined using NMR spectroscopy. The main structural elements of this 42-residue peptide were an anti-parallel β-sheet comprising residues 15-18 and 37-40 and a small 310 helix spanning residues 10-12. The overall three-dimensional fold is similar to that of β-defensin-12, and similar to the sodium-channel neurotoxin ShI (Stichodactyla helianthusneurotoxin I). However, the side chains known to be functionally important in β-defensin-12 and ShI are not conserved in DLP-1, suggesting that it has a different biological function. Consistent with this contention, we showed that DLP-1 possesses no anti-microbial properties and has no observable activity on rat dorsal-root-ganglion sodium-channel currents.

scholarly journals Online biophysical predictions for SARS-CoV-2 proteins

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luciano Kagami ◽  
Joel Roca-Martínez ◽  
Jose Gavaldá-García ◽  
Pathmanaban Ramasamy ◽  
K. Anton Feenstra ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Static Structure ◽  
Homologous Proteins ◽  
Structure Based Drug Design ◽  
Protein Protein Interaction ◽  
Link Type ◽  
Dynamics Simulations ◽  
Β Sheet

Abstract Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. Main We present a website (https://bio2byte.be/sars2/) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. Conclusion The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

The dark and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological function and origin of oxygenase/luciferase activity

2016 ◽  
Vol 15 (5) ◽  
pp. 654-665 ◽  
Author(s):  
R. A. Prado ◽  
C. R. Santos ◽  
D. I. Kato ◽  
M. T. Murakami ◽  
V. R. Viviani
Keyword(s):  
Biological Function ◽  
Luciferase Activity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Catalytic Residue ◽  
Three Dimensional Structure ◽  
Catalytic Activities ◽  
Terminal Domain ◽  
Coa Ligase

The structure and catalytic activities of a Malpighian luciferase-like enzyme indicate a generalistic xenobiotic CoA-ligase and a catalytic residue for bioluminescence.

scholarly journals Solution structure of the strawberry allergen Fra a 1

2012 ◽  
Vol 32 (6) ◽  
pp. 567-575 ◽  
Author(s):  
Christian Seutter von Loetzen ◽  
Kristian Schweimer ◽  
Wilfried Schwab ◽  
Paul Rösch ◽  
Olivia Hartl-Spiegelhauer
Keyword(s):  
Solution Structure ◽  
Three Dimensional ◽  
Protein Family ◽  
Dimensional Structure ◽  
Hydrophobic Pocket ◽  
Pigment Synthesis ◽  
Family Protein ◽  
Pr10 Protein ◽  
Α Helix

The PR10 family protein Fra a 1E from strawberry (Fragaria x ananassa) is down-regulated in white strawberry mutants, and transient RNAi (RNA interference)-mediated silencing experiments confirmed that Fra a 1 is involved in fruit pigment synthesis. In the present study, we determined the solution structure of Fra a 1E. The protein fold is identical with that of other members of the PR10 protein family and consists of a seven-stranded antiparallel β-sheet, two short V-shaped α-helices and a long C-terminal α-helix that encompass a hydrophobic pocket. Whereas Fra a 1E contains the glycine-rich loop that is highly conserved throughout the protein family, the volume of the hydrophobic pocket and the size of its entrance are much larger than expected. The three-dimensional structure may shed some light on its physiological function and may help to further understand the role of PR10 proteins in plants.

CSSP(Consensus Secondary Structure Prediction): a web-based server for structural biologists

2009 ◽  
Vol 42 (2) ◽  
pp. 336-338 ◽  
Author(s):  
Ankit Gupta ◽  
Avnish Deshpande ◽  
Janardhan Kumar Amburi ◽  
Radhakrishnan Sabarinathan ◽  
Ramaswamy Senthilkumar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Web Server ◽  
Dimensional Structure ◽  
Structural Elements ◽  
Web Based ◽  
Consensus Secondary Structure ◽  
Helical Wheel

Sequence–structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

scholarly journals Biochemical mechanism of action of a diketopiperazine inactivator of plasminogen activator inhibitor-1

2003 ◽  
Vol 373 (3) ◽  
pp. 723-732 ◽  
Author(s):  
Anja P. EINHOLM ◽  
Katrine E. PEDERSEN ◽  
Troels WIND ◽  
Paulina KULIG ◽  
Michael T. OVERGAARD ◽  
...  
Keyword(s):  
Plasminogen Activator ◽  
Therapeutic Target ◽  
Three Dimensional ◽  
Plasminogen Activator Inhibitor ◽  
Dimensional Structure ◽  
Plasminogen Activator Inhibitor 1 ◽  
Biochemical Basis ◽  
Β Sheet ◽  
Activator Inhibitor ◽  
Pai 1

XR5118 [(3Z,6Z)-6-benzylidine-3-(5-(2-dimethylaminoethyl-thio-))-2-(thienyl)methylene-2,5-dipiperazinedione hydrochloride] can inactivate the anti-proteolytic activity of the serpin plasminogen activator inhibitor-1 (PAI-1), a potential therapeutic target in cancer and cardiovascular diseases. Serpins inhibit their target proteases by the P1 residue of their reactive centre loop (RCL) forming an ester bond with the active-site serine residue of the protease, followed by insertion of the RCL into the serpin's large central β-sheet A. In the present study, we show that the RCL of XR5118-inactivated PAI-1 is inert to reaction with its target proteases and has a decreased susceptibility to non-target proteases, in spite of a generally increased proteolytic susceptibility of specific peptide bonds elsewhere in PAI-1. The properties of XR5118-inactivated PAI-1 were different from those of the so-called latent form of PAI-1. Alanine substitution of several individual residues decreased the susceptibility of PAI-1 to XR5118. The localization of these residues in the three-dimensional structure of PAI-1 suggested that the XR5118-induced inactivating conformational change requires mobility of α-helix F, situated above β-sheet A, and is in agreement with the hypothesis that XR5118 binds laterally to β-sheet A. These results improve our understanding of the unique conformational flexibility of serpins and the biochemical basis for using PAI-1 as a therapeutic target.

scholarly journals The Structure of Bypass of Forespore C, an Intercompartmental Signaling Factor during Sporulation in Bacillus

2005 ◽  
Vol 280 (43) ◽  
pp. 36214-36220 ◽  
Author(s):  
Hayley M. Patterson ◽  
James A. Brannigan ◽  
Simon M. Cutting ◽  
Keith S. Wilson ◽  
Anthony J. Wilkinson ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Mother Cell ◽  
Asymmetric Cell Division ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Coat Proteins ◽  
Terminal Domain ◽  
Spore Coat Proteins ◽  
Α Helix ◽  
Β Sheet

Sporulation in Bacillus subtilis begins with an asymmetric cell division giving rise to smaller forespore and larger mother cell compartments. Different programs of gene expression are subsequently directed by compartment-specific RNA polymerase σ-factors. In the final stages, spore coat proteins are synthesized in the mother cell under the control of RNA polymerase containing σK, (EσK). σK is synthesized as an inactive zymogen, pro-σK, which is activated by proteolytic cleavage. Processing of pro-σK is performed by SpoIVFB, a metalloprotease that resides in a complex with SpoIVFA and bypass of forespore (Bof)A in the outer forespore membrane. Ensuring coordination of events taking place in the two compartments, pro-σK processing in the mother cell is delayed until appropriate signals are received from the forespore. Cell-cell signaling is mediated by SpoIVB and BofC, which are expressed in the forespore and secreted to the intercompartmental space where they regulate pro-σK processing by mechanisms that are not yet fully understood. Here we present the three-dimensional structure of BofC determined by solution state NMR. BofC is a monomer made up of two domains. The N-terminal domain, containing a four-stranded β-sheet onto one face of which an α-helix is packed, closely resembles the third immunoglobulin-binding domain of protein G from Streptococcus. The C-terminal domain contains a three-stranded β-sheet and three α-helices in a novel domain topology. The sequence connecting the domains contains a conserved DISP motif to which mutations that affect BofC activity map. Possible roles for BofC in the σK checkpoint are discussed in the light of sequence and structure comparisons.

scholarly journals A peptide mimic of an antigenic loop of α-human chorionic gonadotropin hormone: solution structure and interaction with a llama VHH domain

2002 ◽  
Vol 366 (2) ◽  
pp. 415-422 ◽  
Author(s):  
Gilles FERRAT ◽  
Jean-Guillaume RENISIO ◽  
Xavier MORELLI ◽  
Jerry SLOOTSTRA ◽  
Rob MELOEN ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chorionic Gonadotropin ◽  
Human Chorionic Gonadotropin ◽  
Solution Structure ◽  
Three Dimensional ◽  
Conformational Exchange ◽  
Dimensional Structure ◽  
Single Chain ◽  
Α Subunit ◽  
Human Chorionic Gonadotropin Hormone

The X-ray structure of a ternary complex between human chorionic gonadotropin hormone (hCG) and two Fvs recognizing its α and β subunits has been recently determined. The Fvs recognize the elongated hCG molecule by its two ends, one being the Leu-12–Cys-29 loop of the α subunit. We have designed and synthesized a 17-amino-acid peptide (named PepH14) derived from the sequence of this antigenic loop with the purpose of mimicking its three-dimensional structure and its affinity for antibodies. We have determined the solution structure of PepH14 by homonuclear NMR spectroscopy and derived distance restraints. Comparison of this structure with that of the corresponding antigenic loop of α-hCG reveals strong conformational similarities. In particular, the two pairs of residues that establish crucial contacts with the Fv fragment share the same conformation in PepH14 and in the authentic hormone loop. We propose a three-dimensional model of interaction of PepH14 with a llama VHH (VHH-H14) fragment cloned from a single-chain llama immunoglobulin raised against α-hCG. This model has been constrained by the chemical shift variations of the H14 1HN and 15N resonances monitored upon binding with PepH14. Mapping of the backbone chemical shift variations on the VHH structure determined by NMR indicates that PepH14 binds to VHH-H14 and forms a complex using the three complementary determining regions (CDRs). They define a shallow groove encompassing residues Thr-31, Ala-56, Tyr-59 and Trp-104 which have been shown to be in conformational exchange [Renisio, Pérez, Czisch, Guenneugues, Bornet, Frenken, Cambillau and Darbon (2002) Proteins 47, 546–555] and also Phe-37 and Ala-50. This groove is close to the hydrophobic interface area observed between VH and VL domains in Fvs from classical antibodies, which explains the rather lateral binding of PepH14 on the VHH.

scholarly journals Conformational Changes of Spo0F along the Phosphotransfer Pathway

2005 ◽  
Vol 187 (24) ◽  
pp. 8221-8227 ◽  
Author(s):  
Kottayil I. Varughese
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Conformational Changes ◽  
Solution Structure ◽  
Three Dimensional ◽  
Bound State ◽  
Dimensional Structure ◽  
Single Domain Protein ◽  
Secondary Messenger ◽  
Domain Protein ◽  
Apo State

ABSTRACT Spo0F is a secondary messenger in the sporulation phosphorelay, and its structure has been characterized crystallographically in the apo-state, in the metal-bound state, and in an interacting state with a phosphotransferase. Additionally, the solution structure of the molecule has been characterized by nuclear magnetic resonance techniques in the unliganded state and in complex with beryllofluoride. Spo0F is a single-domain protein with a well-defined three-dimensional structure, but it is capable of adapting to specific conformations for catching and releasing the phosphoryl moiety. This commentary deals with the conformational fluctuations of the molecule as it moves from an apo-state to a metal-coordinated state, to a phosphorylated state, and then to a phosphoryl-transferring state.

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