Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison

Proteins
A T Brünger, M Karplus

Abstract

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin, ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.

References

Jun 16, 1977·Nature·J A McCammonM Karplus
Nov 5, 1978·Journal of Molecular Biology·J Janin, S Wodak
Jun 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·B R Gelin, M Karplus
Dec 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·A T BrüngerM Karplus
Aug 15, 1983·Journal of Molecular Biology·M Levitt
Jun 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·A WlodawerL Sjölin
Nov 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Apr 1, 1986·Journal of Computational Chemistry·Scott J WeinerDavid A Case

❮ Previous
Next ❯

Citations

Aug 22, 2000·Biopolymers·C GuilbertJ C Smith
Mar 1, 1990·Biopolymers·M NilgesA M Gronenborn
Dec 24, 2002·Journal of Computational Chemistry·Robert J PetrellaMartin Karplus
Feb 1, 1994·Protein Science : a Publication of the Protein Society·Z S Hendsch, B Tidor
Feb 1, 1997·Protein Science : a Publication of the Protein Society·S T WlodekJ A McCammon
Jan 7, 1998·Protein Science : a Publication of the Protein Society·T LazaridisM Karplus
Mar 26, 1998·Protein Science : a Publication of the Protein Society·L T ChongB Tidor
Jul 9, 1998·Protein Science : a Publication of the Protein Society·S JääskeläinenL S Caves
Oct 7, 1998·Protein Science : a Publication of the Protein Society·V Spassov, D Bashford
Oct 1, 1996·Journal of Computer-aided Molecular Design·A Caflisch
May 25, 2010·European Biophysics Journal : EBJ·Jeremy FidelakRoland H Stote
Jul 28, 2007·Journal of Computer-aided Molecular Design·Erik EvensenMartin Karplus
Sep 27, 1995·Biochimica Et Biophysica Acta·D J BicoutH M Jouve
Jun 1, 1992·Journal of Molecular Graphics·X de la CruzI Fita
Nov 26, 2002·Journal of Molecular Biology·Olivier Michielin, Martin Karplus
May 5, 1998·Molecular Immunology·U LamminmäkiT Lövgren
Jul 14, 2001·Journal of Molecular Graphics & Modelling·S AhmedA Caflisch
Feb 8, 2000·Journal of Molecular Graphics & Modelling·O Galzitskaya, A Caflisch
Aug 6, 2011·Biochemistry·Yao WuEdwin R Chapman
Sep 27, 2012·Journal of Chemical Information and Modeling·Nejc CarlDušanka Janežič
Jul 28, 2007·Journal of the American Chemical Society·Liang Ma, Qiang Cui
Oct 13, 2010·The Journal of Physical Chemistry. B·Jennifer S HirschiVern L Schramm
May 13, 2011·The Journal of Physical Chemistry. B·Maike ClemensMarcus Elstner
Jun 10, 2011·The Journal of Physical Chemistry. B·Mikhail Y WolfsonArup K Chakraborty
Oct 1, 2011·Langmuir : the ACS Journal of Surfaces and Colloids·Tillmann UteschMaria Andrea Mroginski
Oct 12, 2004·Nature Structural & Molecular Biology·B Trevor SewellHelen R Saibil

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Landau-Kleffner Syndrome

Landau Kleffner syndrome (LKS), also called infantile acquired aphasia, acquired epileptic aphasia, or aphasia with convulsive disorder, is a rare childhood neurological syndrome characterized by the sudden or gradual development of aphasia (the inability to understand or express language) and an abnormal electroencephalogram. Discover the latest research on LKS here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.