The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch

Perlecan is a proteoglycan composed of a 470-kDa core protein linked to three heparan sulfate (HS) glycosaminoglycan chains. The intact proteoglycan inhibits the smooth muscle cell (SMC) response to vascular injury. Hspg2Δ3/Δ3 (MΔ3/Δ3) mice produce a mutant perlecan lacking the HS side chains. The objective of this study was to determine differences between these two types of perlecan in modifying SMC activities to the arterial injury response, in order to define the specific role of the HS side chains. In vitro proliferative and migratory activities were compared in SMC isolated from MΔ3/Δ3 and wild-type mice. Proliferation of MΔ3/Δ3 SMC was 1.5× greater than in wild type ( P < 0.001), increased by addition of growth factors, and showed a 42% greater migratory response than wild-type cells to PDGF-BB ( P < 0.001). In MΔ3/Δ3 SMC adhesion to fibronectin, and collagen types I and IV was significantly greater than wild type. Addition of DRL-12582, an inducer of perlecan expression, decreased proliferation and migratory response to PDGF-BB stimulation in wild-type SMC compared with MΔ3/Δ3. In an in vivo carotid artery wire injury model, the medial thickness, medial area/lumen ratio, and macrophage infiltration were significantly increased in the MΔ3/Δ3 mice, indicating a prominent role of the HS side chain in limiting vascular injury response. Mutant perlecan that lacks HS side chains had a marked reduction in the inhibition of in vitro SMC function and the in vivo arterial response to injury, indicating the critical role of HS side chains in perlecan function in the vessel wall.

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Electronic Transport via Homopeptides: The Role of Side Chains and Secondary Structure

Journal of the American Chemical Society ◽

10.1021/jacs.5b03933 ◽

2015 ◽

Vol 137 (30) ◽

pp. 9617-9626 ◽

Cited By ~ 61

Author(s):

Lior Sepunaru ◽

Sivan Refaely-Abramson ◽

Robert Lovrinčić ◽

Yulian Gavrilov ◽

Piyush Agrawal ◽

...

Keyword(s):

Secondary Structure ◽

Electronic Transport ◽

Side Chains

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Uncovering the Role of Key Active Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalysed by Wild-Type and Variants of Triosephosphate Isomerase

10.26434/chemrxiv.9547085.v2 ◽

2019 ◽

Author(s):

Yashraj S. Kulkarni ◽

Tina L. Amyes ◽

John Richard ◽

Shina Caroline Lynn Kamerlin

Keyword(s):

Active Site ◽

Triosephosphate Isomerase ◽

Valence Bond ◽

Side Chains ◽

Wild Type ◽

Empirical Valence Bond

Manuscript and supporting information outlining an analysis of an extended Brønsted relationship obtained from empirical valence bond simulations of substrate deprotonation catalyzed by wild-type and mutant variants of triosephosphate isomerase.

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IN VITRO FERTILITY TEST OF HUMAN SPERMATOZOA MEMBRANE PROTEIN FERTILIN BETA ANTIBODY IN MICE (Mus musculus Balb/c) AS IMMUNOCONTRACEPTIVE CANDIDATE

Folia Medica Indonesiana ◽

10.20473/fmi.v52i3.5453 ◽

2017 ◽

Vol 52 (3) ◽

pp. 209

Author(s):

Reny I’tishom ◽

Doddy M Soebadi ◽

Aucky Hinting ◽

Hamdani Lunardhi ◽

Rina Yudiwati

Keyword(s):

In Vitro Fertilization ◽

Membrane Protein ◽

Mus Musculus ◽

Human Spermatozoa ◽

Control Group ◽

Reproductive Process ◽

Vitro Fertilization ◽

Antibody Induction

One of the materials as potential candidates immunocontraception material is spermatozoa. Fertilin beta is spermatozoa membrane protein and is found only in mature spermatozoa and ejaculate, which serves as an adhesion molecule. Spermatozoa membrane protein that is used as an ingredient immunocontraception candidate, must have specific criteria that the specificity of spermatozoa, the role of antigen in the fertilization process, which includes the formation of immunogenicity sufficient antibody response has the potential to block fertilization. Antibodies against spermatozoa affect the stages before fertilization of the reproductive process and can hinder the development of the embryo after fertilization. Until now very little research data spermatozoa membrane protein as an ingredient immunocontraception are up to the test of experimental animals. The research objective is to prove the role of the resulting antibody induction of antibodies fertilin beta protein in the membrane of human spermatozoa induce agglutination and reduce motility thus reducing the number of in vitro fertilization. Research conducted at the IVF Laboratory, Department of Biology of Medicine, Faculty of Medicine, University of Airlangga. This research includes: Test the potential of antibody protein beta fertilin membrane of human spermatozoa and inhibit the role of antibodies in vitro fertilization in mice (Mus musculus Balb/c). In vitro studies have resulted in fertilization figure of 25% is smaller than the number that is equal to control fertilization of 58.7%, whereas previously the spermatozoa were incubated first with a beta membrane protein antibody fertilin human spermatozoa. While the percentage of inhibition of sperm to fertilize an oocyte by 33.75%. Potential imunokontraseptif considered effective if it decreased significantly (P <0.05) than the numbers fertilization in the treatment group compared with the control group. This shows fertilin beta membrane protein antibody has the ability to inhibit human spermatozoa to fertilize oocytes that reduce the number of fertilization.

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Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

10.1101/2021.01.07.425261 ◽

2021 ◽

Author(s):

Pär Söderhjelm ◽

Mandar Kulkarni

Keyword(s):

Free Energy ◽

Trypsin Inhibitor ◽

Side Chain ◽

Side Chains ◽

Aromatic Residues ◽

Basic Pancreatic Trypsin Inhibitor ◽

Pancreatic Trypsin Inhibitor ◽

Energy Surfaces ◽

Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

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