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Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation

10.03.2015 | Ramkrishna Adhikary; Wayne Yu; Masayuki Oda; Ross C. Walker; Tingjian Chen; Robyn L. Stanfield; Ian A. Wilson; Jörg ..., Biochemistry, 2015

While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an ...


Overexpression in Yeast, Photocycle, and in Vitro Structural Change of an Avian Putative Magnetoreceptor Cryptochrome4

04.03.2015 | Hiromasa Mitsui; Toshinori Maeda; Chiaki Yamaguchi; Yusuke Tsuji; Ryuji Watari; Yoko Kubo; Keiko Okano; Toshiyuki Okano, Biochemistry, 2015

Cryptochromes (CRYs) have been found in a wide variety of living organisms and can function as blue light photoreceptors, circadian clock molecules, or magnetoreceptors. Non-mammalian vertebrates have CRY4 in addition to the CRY1 and CRY2 circadian clock components. Though the function of CRY4 is ...


Analysis of the Radiation-Damage-Free X-ray Structure of Photosystem II in Light of EXAFS and QM/MM Data

27.02.2015 | Mikhail Askerka; David J. Vinyard; Jimin Wang; Gary W. Brudvig; Victor S. Batista, Biochemistry, 2015

A recent femtosecond X-ray diffraction study produced the first high-resolution structural model of the oxygen-evolving complex of photosystem II that is free of radiation-induced manganese reduction (Protein Data Bank entries 4UB6 and 4UB8). We find, however, that the model does not match ...


Mechanistic Insights into the Lipid Interaction of an Ancient Saposin-like Protein

26.02.2015 | Matthias Michalek; Matthias Leippe, Biochemistry, 2015

The members of the expanding family of saposin-like proteins (SAPLIPs) have various biological functions in plants, animals, and humans. In addition to a similar protein backbone, these proteins have in common the fact that they interact with lipid membranes. According to their phylogenetic ...


Circadian Clock and Photoperiodic Response in Arabidopsis: From Seasonal Flowering to Redox Homeostasis

30.12.2014 | Jae Sung Shim; Takato Imaizumi, Biochemistry, 2014

Many of the developmental responses and behaviors in plants that occur throughout the year are controlled by photoperiod; among these, seasonal flowering is the most characterized. Molecular genetic and biochemical analyses have revealed the mechanisms by which plants sense changes in day length ...


Cluster III of Low-Density Lipoprotein Receptor-Related Protein 1 Binds Activated Blood Coagulation Factor VIII

23.12.2014 | James H. Kurasawa; Svetlana A. Shestopal; Samuel A. Woodle; Mikhail V. Ovanesov; Timothy K. Lee; Andrey G. Sarafanov, Biochemistry, 2014

Low-density lipoprotein receptor-related protein 1 (LRP) mediates clearance of blood coagulation factor VIII (FVIII). In LRP, FVIII binds the complement-type repeats (CRs) of clusters II and IV, which also bind a majority of other LRP ligands. No ligand is known for LRP cluster I, and only three ...


Characterizing Substrate Selectivity of Ubiquitin C-Terminal Hydrolase-L3 Using Engineered α-Linked Ubiquitin Substrates

17.12.2014 | Mario F. Navarro; Lisa Carmody; Octavio Romo-Fewell; Melissa E. Lokensgard; John J. Love, Biochemistry, 2014

The ubiquitin-proteasome system (UPS) is highly complex and entails the concerted actions of many enzymes that function to ubiquitinate proteins targeted to the proteasome as well as enzymes that remove and recycle ubiquitin for additional rounds of proteolysis. Ubiquitin C-terminal hydrolase-L3 ...


Probing the Binding Mechanism of Mnk Inhibitors by Docking and Molecular Dynamics Simulations

05.12.2014 | Srinivasaraghavan Kannan; Anders Poulsen; Hai Yan Yang; Melvyn Ho; Shi Hua Ang; Tan Sum Wai Eldwin; Duraiswamy Athis ..., Biochemistry, 2014

Mitogen-activated protein kinases-interacting kinase 1 and 2 (Mnk1/2) activate the oncogene eukaryotic initiation factor 4E (eIF4E) by phosphorylation. High level of phosphorylated eIF4E is associated with various types of cancers. Inhibition of Mnk prevents eIF4E phosphorylation, making them ...


A Synchrotron-Based Hydroxyl Radical Footprinting Analysis of Amyloid Fibrils and Prefibrillar Intermediates with Residue-Specific Resolution

03.12.2014 | Alexandra L. Klinger; Janna Kiselar; Serguei Ilchenko; Hiroaki Komatsu; Mark R. Chance; Paul H. Axelsen, Biochemistry, 2014

Structural models of the fibrils formed by the 40-residue amyloid-β (Aβ40) peptide in Alzheimer’s disease typically consist of linear polypeptide segments, oriented approximately perpendicular to the long axis of the fibril, and joined together as parallel in-register β-sheets to form filaments. ...


Closure of the Cytoplasmic Gate Formed by TM5 and TM11 during Transport in the Oxalate/Formate Exchanger from Oxalobacter formigenes

02.12.2014 | Osigbemhe Iyalomhe; Dawn Z. Herrick; David S. Cafiso; Peter C. Maloney, Biochemistry, 2014

OxlT, the oxalate/formate exchanger of Oxalobacter formigenes, is a member of the major facilitator superfamily of transporters. In the present work, substrate (oxalate) was found to enhance the reactivity of the cysteine mutant S336C on the cytoplasmic end of helix 11 to methanethiosulfonate ...


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