Question: Also known as spirit of nider, what reacts with proteins to form yellow products?

Context paragraphs:
Deubiquitinating enzyme: Deubiquitinating enzymes (DUBs), also known as deubiquitinating peptidases, deubiquitinating isopeptidases, deubiquitinases, ubiquitin proteases, ubiquitin hydrolases, ubiquitin isopeptidases, are a large group of proteases that cleave ubiquitin from proteins and other molecules.  Ubiquitin is attached to proteins in order to regulate the degradation of proteins via the proteasome and lysosome; coordinate the cellular localisation of proteins; activate and inactivate proteins; and modulate protein-protein interactions. DUBs can reverse these effects by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein.  In humans there are nearly 100 DUB genes, which can be classified into two main classes: cysteine proteases and metalloproteases.  The cysteine proteases comprise ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), Machado-Josephin domain proteases (MJDs) and ovarian tumour proteases (OTU).  The metalloprotease group contains only the Jab1/Mov34/Mpr1 Pad1 N-terminal+ (MPN+) (JAMM) domain proteases.

Xanthoproteic acid: Xanthoproteic acid is a noncrystallizable yellow substance derived from proteins upon treatment with nitric acid.  Nitric acid reacts with proteins to form yellow nitrated products.  This reaction is known as the xanthoproteic reaction.  This test is carried out by adding concentrated nitric acid to the substance being tested, and then heating the mixture.  If proteins are present that contains amino acids with aromatic rings, the mixture turns yellow.  Upon adding a strong base such as liquid ammonia, the color turns orange.  These color changes are caused by nitrated aromatic rings in the protein.  The xanthoproteic test is specific for aromatic compounds such as tyrosine, tryptophan and phenyalanine.

Aspartic acid: Aspartic acid (abbreviated as Asp or D; encoded by the codons [GAU and GAC]), also known as aspartate, is an α-amino acid that is used in the biosynthesis of proteins.  Similar to all other amino acids it contains an amino group and a carboxylic acid.  Its α-amino group is in the protonated –NH form under physiological conditions, while its α-carboxylic acid group is deprotonated −COO under physiological conditions.  Aspartic acid has an acidic side chain (CHCOOH) which reacts with other amino acids, enzymes and proteins in the body.  Under physiological conditions (pH 7.4) in proteins the side chain usually occurs as the negatively charged aspartate form, −COO .  It is a non-essential amino acid in humans, meaning the body can synthesize it as needed.

Clathrin adaptor protein: Clathrin adaptor proteins, also known as adaptins, are vesicular transport adaptor proteins associated with clathrin.  These proteins are synthesized in the ribosomes, processed in the endoplasmic reticulum and transported from the Golgi apparatus to the trans-Golgi network, and from there via small carrier vesicles to their final destination compartment.  The association between adaptins and clathrin are important for vesicular cargo selection and transporting.  Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles.  Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration.  The two major types of clathrin adaptor complexes are the heterotetrameric vesicular transport adaptor proteins (AP1-5), and the monomeric GGA (Golgi-localising, Gamma-adaptin ear homology, ARF-binding proteins) adaptors.  Adaptins are distantly related to the other main type of vesicular transport proteins, the coatomer subunits, sharing between 16% and 26% of their amino acid sequence.

Inhibitor of DNA-binding protein: Inhibitor of DNA-binding/differentiation proteins, also known as ID proteins comprise a family of proteins that heterodimerize with basic helix-loop-helix (bHLH) transcription factors to inhibit DNA binding of bHLH proteins.  ID proteins also contain the HLH-dimerization domain but lack the basic DNA-binding domain and thus regulate bHLH transcription factors when they heterodimermize with bHLH proteins.  The first helix-loop-helix proteins identified were named E-proteins because they bind to Ephrussi-box (E-box) sequences.  In normal development, E proteins form dimers with other bHLH transcription factors, allowing transcription to occur.  However, in cancerous phenotypes, ID proteins can regulate transcription by binding E proteins, so no dimers can be formed and transcription is inactive.  E proteins are members of the class I bHLH family and form dimers with bHLH proteins from class II to regulate transctiption.  Four ID proteins exist in humans: ID1, ID2, ID3, and ID4.  The ID homologue gene in Drosophila is called extramacrochaetae (EMC) and encodes a transcription factor of the helix-loop-helix family that lacks a DNA binding domain.  EMC regulates cell proliferation, formation of organs like the midgut, and wing development.  ID proteins could be potential targets for systemic cancer therapies without inhibiting the functioning of most normal cells because they are highly expressed in embryonic stem cells, but not in differentiated adult cells.  Evidence suggests that ID proteins are overexpressed in many types of cancer.  For example, ID1 is overexpressed in pancreatic, breast, and prostate cancers.  ID2 is upregulated in neuroblastoma, Ewing’s sarcoma, and squamous cell carcinoma of the head and neck.

Major urinary proteins: Major urinary proteins (Mups), also known as αu-globulins, are a subfamily of proteins found in abundance in the urine and other secretions of many animals.  Mups provide a small range of identifying information about the donor animal, when detected by the vomeronasal organ of the receiving animal.  They belong to a larger family of proteins known as lipocalins. Mups are encoded by a cluster of genes, located adjacent to each other on a single stretch of DNA, that varies greatly in number between species: from at least 21 functional genes in mice to none in humans.  Mup proteins form a characteristic glove shape, encompassing a ligand-binding pocket that accommodates specific small, organic chemicals.

GTPase-activating protein: GTPase-activating proteins or GTPase-accelerating proteins (GAPs) are a family of regulatory proteins whose members can bind to activated G proteins and stimulate their GTPase activity, with the result of terminating the signaling event.  GAPs are also known as RGS protein, or RGS proteins, and these proteins are crucial in controlling the activity of G proteins.  Regulation of G proteins is important because these proteins are involved in a variety of important cellular processes.  The large G proteins, for example, are involved in transduction of signaling from the G protein-coupled receptor for a variety of signaling processes like hormonal signaling, and small G proteins are involved in processes like cellular trafficking and cell cycling.  GAP’s role in this function is to turn the G protein’s activity off.  In this sense, GAPs function is opposite to that of guanine nucleotide exchange factors (GEFs), which serve to enhance G protein signaling.

Nitric acid: Nitric acid (HNO), also known as aqua fortis and spirit of niter, is a highly corrosive mineral acid.

ARID domain: In molecular biology, the ARID domain (AT-rich interaction domain; also known as BRIGHT domain)) is a protein domain that binds to DNA.  ARID domain-containing proteins are found in fungi, plants and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control.  Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure.  The basic structure of the ARID domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six.  Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

Conalbumin: Ovotransferrin (conalbumin) is a glycoprotein of egg white albumen.  Egg white albumen is composed of multiple proteins and ovotransferrin is the most heat reliable protein of them all.  It has a molecular weight of 76,000 daltons and contains about 700 amino acids. Ovotransferrin makes up approximately 13% of egg albumen (in contrast to ovalbumin, which comprises 54%).  As a member of the transferrin and metalloproteinase family, ovotransferrin has been found to produce heat shock proteins.  When these heat shock proteins are induced in the skin, they provide protection against cold stress and other environmental stresses.  Ovotransferrin is folded in a way that forms two lobes (N- and C- terminals) and each lobe consists of a binding site.  Each lobe is then divided into two domains of 160 amino acid residues.  Its structure also consists of fifteen disulfide crosslinks and no free sulfhydryl groups.  Disulfide groups stabilize the tertiary structures of proteins.  Transferrins, are iron binding proteins and acute phase reactants of animal serum.  It has a binding log of 15 at a pH of 7 or above, meaning that the iron binding capacity of ovotransferrin rapidly decreased at a pH that is less than 6.  This family is also known for their role in cell maturation by transporting essential nutrients to developing embryos.  Ovotransferrin functions as an antimicrobial agent and transports iron to the developing embryo.  Because they bind to iron, this makes it difficult for harmful bacteria to be nutritionally satisfied with them so it acts as an antimicrobial.

Supporting paragraphs: Xanthoproteic acid Nitric acid
Answer: Nitric acid