BIOMAT Database Logo BIOMAT Database Logo

Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68-107) by NMR spectroscopy and MD simulations. 2022

Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Kazan Federal University, Kremlevskaya Str., 18, 420008 Kazan, Russian Federation.

SEM1(68-107) is a peptide corresponding to the region of semenogelin 1 protein from 68 to 107 amino acid position. SEM1(68-107) is an abundant component of semen, which participates in HIV infection enhanced by amyloid fibrils forming. To understand the causes influencing amyloid fibril formation, it is necessary to determine the spatial structure of SEM1(68-107). It was shown that the determination of SEM1(68-107) structure is complicated by the non-informative NMR spectra due to the high intramolecular mobility of peptides. The complementary approach based on the geometric restrictions of individual peptide fragments and molecular modeling was used for the determination of the spatial structure of SEM1(68-107). The N- (SEM1(68-85)) and C-terminuses (SEM1(86-107)) of SEM1(68-107) were chosen as two individual peptide fragments. SEM1(68-85) and SEM1(86-107) structures were established with NMR and circular dichroism CD spectroscopies. These regions were used as geometric restraints for the SEM1(68-107) structure modeling. Even though most of the SEM1(68-107) peptide is unstructured, our detailed analysis revealed the following structured elements: N-terminus (70His-84Gln) forms an α-helix, (86Asp-94Thr) and (101Gly-103Ser) regions fold into 310-helixes. The absence of a SEM1(68-107) rigid conformation leads to instability of these secondary structure regions. The calculated SEM1(68-107) structure is in good agreement with experimental values of hydrodynamic radius and dihedral angles obtained by NMR spectroscopy. This testifies the adequacy of a combined approach based on the use of peptide fragment structures for the molecular modeling formation of full-size peptide spatial structure.

UI MeSH Term Description Entries
D009682 Magnetic Resonance Spectroscopy Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING). In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D010446 Peptide Fragments Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques. Peptide Fragment,Fragment, Peptide,Fragments, Peptide
D010455 Peptides Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are considered to be larger versions of peptides that can form into complex structures such as ENZYMES and RECEPTORS. Peptide,Polypeptide,Polypeptides
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000682 Amyloid A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease. Amyloid Fibril,Amyloid Fibrils,Amyloid Substance,Fibril, Amyloid,Fibrils, Amyloid,Substance, Amyloid
D015658 HIV Infections Includes the spectrum of human immunodeficiency virus infections that range from asymptomatic seropositivity, thru AIDS-related complex (ARC), to acquired immunodeficiency syndrome (AIDS). HTLV-III Infections,HTLV-III-LAV Infections,T-Lymphotropic Virus Type III Infections, Human,HIV Coinfection,Coinfection, HIV,Coinfections, HIV,HIV Coinfections,HIV Infection,HTLV III Infections,HTLV III LAV Infections,HTLV-III Infection,HTLV-III-LAV Infection,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,T Lymphotropic Virus Type III Infections, Human

Related Publications

Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
The data of heterologous expression protocol for synthesis of 15N, 13C-labeled SEM1(68-107) peptide fragment of homo sapiens semenogelin 1.
January 2021, MethodsX,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs.
January 2021, International journal of molecular sciences,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Conformation of N-terminal HIV-1 Tat (fragment 1-9) peptide by NMR and MD simulations.
November 2001, Journal of peptide science : an official publication of the European Peptide Society,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
pH effects on the conformational preferences of amyloid beta-peptide (1-40) in HFIP aqueous solution by NMR spectroscopy.
May 2008, ChemMedChem,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Conformational analysis of methyl beta-cellobioside by ROESY NMR spectroscopy and MD simulations in combination with the CROSREL method.
July 1993, Carbohydrate research,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Structural characterization of semen coagulum-derived SEM1(86-107) amyloid fibrils that enhance HIV-1 infection.
May 2014, Biochemistry,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Epigallocatechin-3-gallate rapidly remodels PAP85-120, SEM1(45-107), and SEM2(49-107) seminal amyloid fibrils.
August 2015, Biology open,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy.
March 2022, Journal of chemical theory and computation,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations.
September 2022, International journal of molecular sciences,
Daria Sanchugova, and Aleksandra Kusova, and Aydar Bikmullin, and Aydar Yulmetov, and Timur Mukhametzyanov, and Vladimir Klochkov, and Dmitriy Blokhin
Conformational studies of RGDechi peptide by natural-abundance NMR spectroscopy.
May 2019, Journal of peptide science : an official publication of the European Peptide Society,
Copied contents to your clipboard!