Gaussian software to know charge of binding pocket

During the repairing process, UDG detects the damaged DNA base pair AU in a double-stranded DNA by identifying the unusual kink of 45В° ( Satange et al., 2018).

In the DNA duplication process, uracil bases occur due to cytosine deamination or deoxy uridine monophosphate (dUMP) residue misincorporation during DNA synthesis ( Longo et al., 1990 Schormann et al., 2014), which leads to a change in the base pair of guanine-cytosine (GC) to adenine-uracil (AU), and over 50% of all the progeny DNA are affected at the mutation site ( Pearl, 2000). Uracil-DNA glycosylase (UDG) is one of the most important enzymes in the BER process ( Lindahl, 1993 Schormann et al., 2014). Among these mechanisms, BER is the process of removing damaged bases which may cause mutations by mispairing or even result in DNA damage ( Liu et al., 2007). DNA repair is an important mechanism that includes base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR) ( Wood et al., 2001 Helleday et al., 2008).

Many studies ( Acharya, 1972 Capri et al., 2006) have shown that several lifespan-influenced genes turn out to be related to DNA damage repair and protection. To keep cells functioning normally, DNA repair is an essential process as it provides comprehensive coverage of cellular responses to DNA damage.

It may be caused by endogenous damages, such as reactive oxygen species (ROS), and exogenous damages, such as X-ray and UV radiation, plant toxins, and viruses ( Jackson and Bartek, 2009). Our results show that the whole UDG binding interface, and not the UDG binding pocket area alone, provides the binding attractive force to the damaged DNA at the uracil base.ДNA damage happens with a rate of ten thousand to one million molecular lesions per cell every day ( Alberts, 2008). Here we applied multiple computational methods to study UDG in several perspectives: Understanding the stability of the UDG enzyme in different pH conditions studying the differences in charge distribution between the pocket side and non-pocket side of UDG analyzing the field line distribution at the interfacial area between UDG and DNA and performing electrostatic binding force analyses of the special region of UDG (pocket area) and the target DNA base (uracil) as well as investigating the charged residues on the UDG binding pocket and binding interface. Therefore, the research of UDG is crucial in cancer treatment and prevention as well as other clinical activities. Medical evidences show that an abnormal expression of UDG is related to different types of cancer, including colorectal cancer, lung cancer, and liver cancer. Uracil in DNA may occur due to cytosine deamination or deoxy uridine monophosphate (dUMP) residue misincorporation during DNA synthesis. Uracil-DNA glycosylase (UDG) is one of the most important base excision repair (BER) enzymes involved in the repair of uracil-induced DNA lesion by removing uracil from the damaged DNA. 4Department of Physics, University of Texas at El Paso, El Paso, TX, United States.3Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States.2Computer Science Program, Santa Monica College, Santa Monica, CA, United States.1Computational Science Program, University of Texas at El Paso, El Paso, TX, United States.Karki 1, Jiawei Chen 2, Dongfang Liu 3 and Lin Li 1,4*

Gaussian software to know charge of binding pocket